Tutorial: eQTL Analysis with SAIGE-QTL using cellink#
This tutorial demonstrates how to perform eQTL analysis using SAIGE-QTL through the cellink package. SAIGE-QTL uses a Poisson mixed model that accounts for sample relatedness and is particularly well-suited for single-cell eQTL analysis. It also accounts for sample relatedness through genetic relationship matrices, handles both common and rare variant analysis and supports cell-level and individual-level covariates. This notebook assumes familiarity with single-cell data processing and basic statistical genetics concepts. The cellink package provides convenient wrapper functions that handle data preparation and formatting for SAIGE-QTL. For the installation please refer to the docs of SAIGE-QTL. We recommend using the provided Docker container.
SAIGE-QTL analysis consists of three steps:
Step 1: Fit null Poisson mixed model (one per gene)
Step 2: Perform association tests (single-variant or set-based)
Step 3 (optional): Calculate gene-level p-values using ACAT
SAIGE-QTL has a range of further options, such as set-based analysis, genome-wide analysis with LOCO or conditional analysis, which are alll supported in the cellink wrapper. For more details please however refer to the docs of SAIGE-QTL.
Environment Setup#
import scanpy as sc
from cellink.resources import get_dummy_onek1k
from cellink.tl.external import run_saigeqtl, configure_saigeqtl_runner
# Analysis parameters
n_gpcs = 20
n_epcs = 15
chrom = 22
cis_window = 500_000
cell_type = "CD8 Naive"
celltype_key = "predicted.celltype.l2"
Configure SAIGE-QTL Runner#
The runner handles execution across different environments (local, docker, singularity):
runner = configure_saigeqtl_runner("../../src/cellink/tl/external/config/saigeqtl_docker.yaml")
Load and Prepare Data#
dd = get_dummy_onek1k(config_path="../../src/cellink/resources/config/dummy_onek1k.yaml", verify_checksum=False)
print(f"Dataset shape: {dd.shape}")
dd.G.obsm["gPCs"] = dd.G.obsm["gPCs"][dd.G.obsm["gPCs"].columns[:n_gpcs]]
dd.aggregate(obs=["donor_id", "sex", "age"], func="first", add_to_obs=True)
dd = dd[..., dd.C.obs[celltype_key] == cell_type, :].copy()
print(f"After cell type filtering: {dd.shape}")
dd.G.obs["donor_sex"] = dd.G.obs["sex"]
dd.G.obs["donor_age"] = dd.G.obs["age"]
dd = dd.sel(G_var=dd.G.var.chrom == str(chrom), C_var=dd.C.var.chrom == str(chrom)).copy()
print(f"After chromosome {chrom} filtering: {dd.shape}")
dd = dd[:, dd.G.var["pos"] < 17584955, :, :].copy()
[2026-01-09 01:39:30,021] INFO:root: /Users/larnoldt/cellink_data/dummy_onek1k/dummy_onek1k.dd.h5 already exists
[2026-01-09 01:39:30,022] WARNING:root: No checksum provided, skipping verification
[2026-01-09 01:39:31,204] INFO:root: Loaded dummy OneK1K dataset: (100, 146939, 125366, 34073)
Dataset shape: (100, 146939, 125366, 34073)
After cell type filtering: (100, 146939, 4756, 34073)
After chromosome 22 filtering: (100, 136776, 4756, 871)
Analysis Workflows#
1. Basic cis-eQTL Analysis (Single-Variant Tests, Steps 1 + 2)#
The most common use case: fit null model and run association tests.
results = run_saigeqtl(
dd,
gene_col="ENSG00000273362", # Gene ID from expression data
prefix="saigeqtl_complete",
steps=[1, 2],
mode="cis",
analysis_type="single_variant",
window=cis_window,
min_mac=20,
sample_covariates=["gPCs"],
use_grm_to_fit_null=False,
overwrite_variance_ratio_file=True,
run=True,
)
results.head()
Writing FAM... done.
Writing BIM... done.
[2026-01-09 01:39:32,509] INFO:cellink.tl.external._saigeqtl: Running Step 1: Fitting null model
[2026-01-09 01:39:32,510] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step1_fitNULLGLMM_qtl.R --phenoFile=saigeqtl_complete_phenotype.txt --phenoCol=ENSG00000273362 --sampleIDColinphenoFile=IND_ID --traitType=count --plinkFile=saigeqtl_complete --outputPrefix=saigeqtl_complete --LOCO=FALSE --useGRMtoFitNULL=FALSE --IsOverwriteVarianceRatioFile=TRUE --covarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19 --sampleCovarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19
[2026-01-09 01:39:49,461] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] optparse_1.7.5 SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] data.table_1.17.6 RcppParallel_5.1.9 lattice_0.22-7
$plinkFile
[1] "saigeqtl_complete"
$bedFile
[1] ""
$bimFile
[1] ""
$famFile
[1] ""
$phenoFile
[1] "saigeqtl_complete_phenotype.txt"
$phenoCol
[1] "ENSG00000273362"
$isRemoveZerosinPheno
[1] FALSE
$traitType
[1] "count"
$invNormalize
[1] FALSE
$covarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19"
$sampleCovarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19"
$longlCol
[1] ""
$qCovarColList
[1] ""
$sampleIDColinphenoFile
[1] "IND_ID"
$cellIDColinphenoFile
[1] ""
$tol
[1] 0.02
$maxiter
[1] 20
$tolPCG
[1] 1e-05
$maxiterPCG
[1] 500
$nThreads
[1] 1
$SPAcutoff
[1] 2
$numRandomMarkerforVarianceRatio
[1] 30
$skipModelFitting
[1] FALSE
$skipVarianceRatioEstimation
[1] FALSE
$memoryChunk
[1] 2
$tauInit
[1] "0,0"
$LOCO
[1] FALSE
$isLowMemLOCO
[1] FALSE
$traceCVcutoff
[1] 0.0025
$nrun
[1] 30
$ratioCVcutoff
[1] 0.001
$outputPrefix
[1] "saigeqtl_complete"
$outputPrefix_varRatio
[1] ""
$IsOverwriteVarianceRatioFile
[1] TRUE
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$isCateVarianceRatio
[1] FALSE
$relatednessCutoff
[1] 0
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$isCovariateTransform
[1] TRUE
$isDiagofKinSetAsOne
[1] FALSE
$useSparseGRMtoFitNULL
[1] FALSE
$useSparseGRMforVarRatio
[1] FALSE
$minMAFforGRM
[1] 0.01
$maxMissingRateforGRM
[1] 0.15
$minCovariateCount
[1] -1
$includeNonautoMarkersforVarRatio
[1] FALSE
$FemaleOnly
[1] FALSE
$MaleOnly
[1] FALSE
$sexCol
[1] ""
$FemaleCode
[1] "1"
$MaleCode
[1] "0"
$isCovariateOffset
[1] TRUE
$SampleIDIncludeFile
[1] ""
$VmatFilelist
[1] ""
$VmatSampleFilelist
[1] ""
$useGRMtoFitNULL
[1] FALSE
$isStoreSigma
[1] TRUE
$isShrinkModelOutput
[1] TRUE
$isExportResiduals
[1] FALSE
$help
[1] FALSE
tauInit is 0 0
cateVarRatioMinMACVecExclude is 10 20.5
cateVarRatioMaxMACVecInclude is 20.5
No GRM will be used to fit the NULL model and nThreads is set to 1
The variance ratio file saigeqtl_complete.varianceRatio.txt already exists. IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten
100 samples have genotypes
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
[1] "HERERE2"
formula is ENSG00000273362~sex+age+gPCs_0+gPCs_1+gPCs_2+gPCs_3+gPCs_4+gPCs_5+gPCs_6+gPCs_7+gPCs_8+gPCs_9+gPCs_10+gPCs_11+gPCs_12+gPCs_13+gPCs_14+gPCs_15+gPCs_16+gPCs_17+gPCs_18+gPCs_19
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
4756 samples have non-missing phenotypes
Duplicated sample IDs are detected in the phenotype file. Assuming repeated measurements
[1] "Test"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
4756 observations will be used for analysis
[1] "Test3"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "Test4"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
qr transformation has been performed on covariates
colnames(data.new) is ENSG00000273362 minus1 sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19
out.transform$Param.transform$qrr: 23 23
[1] "isCovariateOffset=TRUE, so fixed effects coefficnets won't be estimated."
[1] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806"
[6] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_518"
[11] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[16] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[21] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[26] "OneK1K_518" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[31] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[36] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[41] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[46] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[51] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[56] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[61] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[66] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[71] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[76] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[81] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[86] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[91] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_588"
[96] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[101] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[106] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[111] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[116] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[121] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[126] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_1061" "OneK1K_1061"
[131] "OneK1K_1061" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[136] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[141] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[146] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[151] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[156] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[161] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[166] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[171] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[176] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[181] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[186] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[191] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[196] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[1] TRUE
numofV 0
[1] "HERE"
[1] "HERE1"
[1] FALSE
num_Kmat 2
ptr_gNULLGENOobj->g_minMACVarRatio 20
ptr_gNULLGENOobj->g_maxMACVarRatio -1
Markers in the Plink file with MAF < 0.01 will be removed before constructing GRM
Markers in the Plink file with missing rate > 0.15 will be removed before constructing GRM
ENSG00000273362 is a count trait
glm:
Call: glm(formula = formula.new, family = "poisson", data = data.new,
weights = varWeights, offset = covoffset)
Coefficients:
(Intercept)
-27.3
Degrees of Freedom: 4755 Total (i.e. Null); 4755 Residual
Null Deviance: 2.42e-10
Residual Deviance: 1.321e-08 AIC: 2
[1] "isStoreSigma"
[1] TRUE
Start fitting the NULL GLMM
user system elapsed
13.890 2.067 15.842
user system elapsed
13.947 2.067 15.900
[1] "Start reading genotype plink file here"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "length(indicatorGenoSamplesWithPheno)"
[1] 4756
[1] "Genotype reading is done"
tauInit[1] 0 0
fixtau 1 0
tauInit 1 0
inital tau is 1 0.1
[1] "tau"
[1] 1.0 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
(Intercept)
-27.30259
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
[1] "tau0_q2 a"
[1] 0.1
[1] "idxtau"
[1] 2
[1] "re$YPAPY"
[,1]
[1,] 1.039092e-18
[1] "re$Trace"
[,1]
[1,] 2.303134e-09
Variance component estimates:
[1] 1.0 0.1
Iteration 1 1 0.1 :
tau0_v1: 1 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
t_end_Get_Coef - t_begin_Get_Coef
user system elapsed
0.000 0.001 0.001
check 1
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
check 2
score1
-2.3031e-09
YPAPY
1.0391e-18
Trace
2.3031e-09
score
-2.3031e-09
i 0
i 1
t_end_fitglmmaiRPCG - t_begin_fitglmmaiRPCG
user system elapsed
0.030 0.001 0.032
[1] 0.000000e+00 6.773277e-09
tau: 1 0.1
tau0: 1 0.1
Final 1 0.1 :
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
4.1159e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -29.30295
[1] "alpha"
[,1]
[1,] -29.30295
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -29.30295
t_end_null - t_begin, fitting the NULL model without LOCO took
user system elapsed
0.090 0.010 0.099
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
isStoreSigma is TRUE
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
user system elapsed
14.047 2.078 16.010
t_end - t_begin, fitting the NULL model took
user system elapsed
0.157 0.011 0.168
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[25] 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[49] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[73] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4
[97] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
[121] 4 4 4 4 4 4 4 4 5 5 5 6 6 6 6 6 6 6 6 6 6 6 6 6
[145] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[169] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[193] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[217] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[241] 6 6 6 6 6 6 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[265] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[289] 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 9 9
[313] 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 10
[337] 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11
[361] 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 13 13 13 13
[385] 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
[409] 13 13 14 14 14 14 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16
[433] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17
[457] 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18
[481] 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 19 19 19 19 19 19
[505] 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19
[529] 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[553] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[577] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[601] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[625] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[649] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[673] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[697] 20 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22
[721] 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22
[745] 22 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
[769] 23 23 23 23 23 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24
[793] 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 25 25 25 25 25
[817] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[841] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[865] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[889] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[913] 26 26 26 26 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[937] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[961] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[985] 27 27 27 27 27 27 27 27 28 28 28 28 28 28 28 28
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "HEREHRE"
nbyte: 25
nbyte: 25
reserve: 115479
M: 4277, N: 100
setgeno mark1
setgeno mark2
3516 markers with MAF >= 0.01 and missing rate <= 0.15
time: 10.171
Start estimating variance ratios
Family: poisson
Link function: log
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
length(MACvector): 3516
length(MACvector_forVarRatio): 521
Only one variance ratio will be estimated using randomly selected markers with MAC >= 20
29 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
257 22 22_16708242_C_T 0 16708242 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2505
iter from getPCG1ofSigmaAndVector 1
AC 2354
S is -2.447558e-24
var1 is 1.911061e-10
p_exact 1
var2sparseGRM Here 1.911062e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2354
var1 1.911061e-10
var2null 1.911061e-10
var2null_noXadj 2.620976e-10
98 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
732 22 22_16849519_G_T 0 16849519 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1548
iter from getPCG1ofSigmaAndVector 1
AC 3852
S is -1.19253e-24
var1 is 2.561159e-10
p_exact 1
var2sparseGRM Here 2.561161e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3852
var1 2.561159e-10
var2null 2.561159e-10
var2null_noXadj 3.799173e-10
45 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
365 22 22_16743395_C_A 0 16743395 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1778
S is -5.863572e-25
var1 is 2.020268e-10
p_exact 1
var2sparseGRM Here 2.02027e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1778
var1 2.020268e-10
var2null 2.020268e-10
var2null_noXadj 2.794007e-10
156 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1141 22 22_16962373_T_A 0 16962373 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
377 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 0 0 2 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2888 22 22_17318326_C_T 0 17318326 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3016
iter from getPCG1ofSigmaAndVector 1
AC 1958
S is 1.091594e-24
var1 is 1.748766e-10
p_exact 1
var2sparseGRM Here 1.748766e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1958
var1 1.748766e-10
var2null 1.748766e-10
var2null_noXadj 3.004277e-10
202 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1670 22 22_17087008_A_G 0 17087008 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
228 th marker in geno 1
MAC: 97
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 0 1 1 2 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1820 22 22_17125423_C_CA 0 17125423 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1434
iter from getPCG1ofSigmaAndVector 1
AC 4638
S is 3.054671e-24
var1 is 3.272003e-10
p_exact 1
var2sparseGRM Here 3.272005e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4638
var1 3.272003e-10
var2null 3.272003e-10
var2null_noXadj 5.172127e-10
212 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 1 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1729 22 22_17106625_T_C 0 17106625 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3123
iter from getPCG1ofSigmaAndVector 1
AC 1761
S is 7.608911e-25
var1 is 1.584355e-10
p_exact 1
var2sparseGRM Here 1.584355e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1761
var1 1.584355e-10
var2null 1.584355e-10
var2null_noXadj 2.572716e-10
492 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4005 22 22_17525225_C_T 0 17525225 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
477 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3916 22 22_17511574_A_G 0 17511574 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3747
iter from getPCG1ofSigmaAndVector 1
AC 1077
S is -3.20694e-25
var1 is 1.279881e-10
p_exact 1
var2sparseGRM Here 1.279882e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1077
var1 1.279881e-10
var2null 1.279882e-10
var2null_noXadj 1.820916e-10
209 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 2 2 2 2 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1717 22 22_17104551_C_T 0 17104551 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1403
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is -2.857582e-24
var1 is 2.749479e-10
p_exact 1
var2sparseGRM Here 2.749481e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 2.749479e-10
var2null 2.749479e-10
var2null_noXadj 4.93364e-10
291 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2303 22 22_17195422_G_A 0 17195422 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3534
iter from getPCG1ofSigmaAndVector 1
AC 1575
S is 7.4808e-25
var1 is 1.891389e-10
p_exact 1
var2sparseGRM Here 1.891391e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1575
var1 1.891389e-10
var2null 1.89139e-10
var2null_noXadj 3.397109e-10
81 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
614 22 22_16822493_C_T 0 16822493 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1281
iter from getPCG1ofSigmaAndVector 1
AC 4492
S is 2.095215e-24
var1 is 2.637957e-10
p_exact 1
var2sparseGRM Here 2.637958e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4492
var1 2.637957e-10
var2null 2.637957e-10
var2null_noXadj 4.479227e-10
79 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
605 22 22_16821873_G_C 0 16821873 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1830
iter from getPCG1ofSigmaAndVector 1
AC 3568
S is -5.426227e-25
var1 is 2.250768e-10
p_exact 1
var2sparseGRM Here 2.250769e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3568
var1 2.250768e-10
var2null 2.250768e-10
var2null_noXadj 4.34582e-10
509 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 2 0 0 2 2 0 1 2 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 0
CHR 22
V1 V2 V3 V4 V5 V6
4190 22 22_17564857_C_CAAAAAAAAAAA 0 17564857 C CAAAAAAAAAAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1354
iter from getPCG1ofSigmaAndVector 1
AC 4575
S is 3.475128e-24
var1 is 2.746995e-10
p_exact 1
var2sparseGRM Here 2.746996e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4575
var1 2.746995e-10
var2null 2.746995e-10
var2null_noXadj 4.758986e-10
496 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 0 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4033 22 22_17531010_A_G 0 17531010 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3289
iter from getPCG1ofSigmaAndVector 1
AC 1622
S is 6.507787e-25
var1 is 1.798199e-10
p_exact 1
var2sparseGRM Here 1.7982e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1622
var1 1.798199e-10
var2null 1.798199e-10
var2null_noXadj 2.604154e-10
362 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2803 22 22_17302684_T_C 0 17302684 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1501
iter from getPCG1ofSigmaAndVector 1
AC 4307
S is 7.681612e-25
var1 is 2.50358e-10
p_exact 1
var2sparseGRM Here 2.503581e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4307
var1 2.50358e-10
var2null 2.50358e-10
var2null_noXadj 4.72288e-10
64 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
518 22 22_16801041_G_A 0 16801041 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3889
S is 4.154646e-25
var1 is 2.153042e-10
p_exact 1
var2sparseGRM Here 2.153043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3889
var1 2.153042e-10
var2null 2.153042e-10
var2null_noXadj 4.40872e-10
440 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3510 22 22_17441874_G_C 0 17441874 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
511 th marker in geno 1
MAC: 74
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4205 22 22_17567322_A_G 0 17567322 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2171
iter from getPCG1ofSigmaAndVector 1
AC 3183
S is 2.085471e-24
var1 is 2.680107e-10
p_exact 1
var2sparseGRM Here 2.680108e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3183
var1 2.680107e-10
var2null 2.680107e-10
var2null_noXadj 4.2986e-10
489 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3985 22 22_17523014_A_AGGGG 0 17523014 A AGGGG
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2724
iter from getPCG1ofSigmaAndVector 1
AC 2268
S is -2.175552e-24
var1 is 1.469711e-10
p_exact 1
var2sparseGRM Here 1.469711e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2268
var1 1.469711e-10
var2null 1.469711e-10
var2null_noXadj 3.283367e-10
216 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1738 22 22_17108677_C_T 0 17108677 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2975
iter from getPCG1ofSigmaAndVector 1
AC 2053
S is -4.137071e-25
var1 is 2.373018e-10
p_exact 1
var2sparseGRM Here 2.373018e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2053
var1 2.373018e-10
var2null 2.373018e-10
var2null_noXadj 3.438314e-10
78 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
600 22 22_16821568_C_G 0 16821568 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3305
iter from getPCG1ofSigmaAndVector 1
AC 1503
S is 8.573971e-26
var1 is 1.270707e-10
p_exact 1
var2sparseGRM Here 1.270707e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1503
var1 1.270707e-10
var2null 1.270707e-10
var2null_noXadj 2.128624e-10
444 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3537 22 22_17445692_G_A 0 17445692 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
227 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1819 22 22_17125117_T_TA 0 17125117 T TA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2824
iter from getPCG1ofSigmaAndVector 1
AC 2307
S is -8.466181e-25
var1 is 2.682152e-10
p_exact 1
var2sparseGRM Here 2.682154e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2307
var1 2.682152e-10
var2null 2.682152e-10
var2null_noXadj 3.641289e-10
259 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2094 22 22_17170409_AAAAAAT_A 0 17170409 AAAAAAT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1738
S is 8.149564e-25
var1 is 1.690214e-10
p_exact 1
var2sparseGRM Here 1.690214e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1738
var1 1.690214e-10
var2null 1.690214e-10
var2null_noXadj 2.678111e-10
40 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
334 22 22_16738360_T_A 0 16738360 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3614
iter from getPCG1ofSigmaAndVector 1
AC 1214
S is 6.221904e-25
var1 is 1.265151e-10
p_exact 1
var2sparseGRM Here 1.265152e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1214
var1 1.265151e-10
var2null 1.265151e-10
var2null_noXadj 1.974943e-10
15 th marker in geno 1
MAC: 58
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
164 22 22_16678727_G_A 0 16678727 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2401
iter from getPCG1ofSigmaAndVector 1
AC 2703
S is -1.590546e-24
var1 is 2.318528e-10
p_exact 1
var2sparseGRM Here 2.318529e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2703
var1 2.318528e-10
var2null 2.318528e-10
var2null_noXadj 3.508839e-10
211 th marker in geno 1
MAC: 94
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 1 1 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1725 22 22_17105724_G_C 0 17105724 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1308
iter from getPCG1ofSigmaAndVector 1
AC 4560
S is -4.742897e-24
var1 is 2.787683e-10
p_exact 1
var2sparseGRM Here 2.787684e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4560
var1 2.787683e-10
var2null 2.787683e-10
var2null_noXadj 4.662892e-10
261 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2123 22 22_17173199_C_T 0 17173199 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2696
S is 1.41061e-24
var1 is 1.886188e-10
p_exact 1
var2sparseGRM Here 1.886189e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2696
var1 1.886188e-10
var2null 1.886188e-10
var2null_noXadj 2.770454e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229
CV for variance ratio estimate using 30 markers is 0.004253911 > 0.001
try 40 markers
269 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2164 22 22_17175884_G_GT 0 17175884 G GT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2696
S is 1.41061e-24
var1 is 1.886188e-10
p_exact 1
var2sparseGRM Here 1.886189e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2696
var1 1.886188e-10
var2null 1.886188e-10
var2null_noXadj 2.770454e-10
38 th marker in geno 1
MAC: 83
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 0 1 1 1 2 0 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
306 22 22_16726908_G_T 0 16726908 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1525
iter from getPCG1ofSigmaAndVector 1
AC 4262
S is -3.97543e-24
var1 is 3.594641e-10
p_exact 1
var2sparseGRM Here 3.594645e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4262
var1 3.594641e-10
var2null 3.594641e-10
var2null_noXadj 4.744979e-10
118 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
862 22 22_16878208_T_C 0 16878208 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2847
iter from getPCG1ofSigmaAndVector 1
AC 1980
S is -7.3306e-25
var1 is 1.541723e-10
p_exact 1
var2sparseGRM Here 1.541723e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1980
var1 1.541723e-10
var2null 1.541723e-10
var2null_noXadj 2.521049e-10
19 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
181 22 22_16688797_GAA_G 0 16688797 GAA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3137
iter from getPCG1ofSigmaAndVector 1
AC 1789
S is 4.323084e-25
var1 is 1.838207e-10
p_exact 1
var2sparseGRM Here 1.838208e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1789
var1 1.838207e-10
var2null 1.838207e-10
var2null_noXadj 2.737403e-10
107 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
790 22 22_16861810_T_C 0 16861810 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3636
iter from getPCG1ofSigmaAndVector 1
AC 1202
S is -2.370843e-26
var1 is 1.168809e-10
p_exact 1
var2sparseGRM Here 1.168809e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1202
var1 1.168809e-10
var2null 1.168809e-10
var2null_noXadj 2.036159e-10
372 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 0 2 0 0 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 2
CHR 22
V1 V2 V3 V4 V5 V6
2861 22 22_17310674_T_C 0 17310674 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2208
iter from getPCG1ofSigmaAndVector 1
AC 2942
S is 3.683324e-24
var1 is 2.37273e-10
p_exact 1
var2sparseGRM Here 2.372732e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2942
var1 2.37273e-10
var2null 2.37273e-10
var2null_noXadj 3.596099e-10
514 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4215 22 22_17570571_G_T 0 17570571 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2123
iter from getPCG1ofSigmaAndVector 1
AC 3527
S is -5.723167e-24
var1 is 2.967774e-10
p_exact 1
var2sparseGRM Here 2.967775e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3527
var1 2.967774e-10
var2null 2.967774e-10
var2null_noXadj 5.084939e-10
67 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
539 22 22_16805822_T_A 0 16805822 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3889
S is 4.154646e-25
var1 is 2.153042e-10
p_exact 1
var2sparseGRM Here 2.153043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3889
var1 2.153042e-10
var2null 2.153042e-10
var2null_noXadj 4.40872e-10
130 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
949 22 22_16914834_C_G 0 16914834 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3590
iter from getPCG1ofSigmaAndVector 1
AC 1238
S is 6.451746e-25
var1 is 1.24676e-10
p_exact 1
var2sparseGRM Here 1.246761e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1238
var1 1.24676e-10
var2null 1.24676e-10
var2null_noXadj 1.994771e-10
248 th marker in geno 1
MAC: 55
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1975 22 22_17151727_TAAAAAA_T 0 17151727 TAAAAAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2655
iter from getPCG1ofSigmaAndVector 1
AC 2315
S is 2.469905e-24
var1 is 2.237693e-10
p_exact 1
var2sparseGRM Here 2.237694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2315
var1 2.237693e-10
var2null 2.237694e-10
var2null_noXadj 3.084451e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755
CV for variance ratio estimate using 40 markers is 0.003165943 > 0.001
try 50 markers
263 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2136 22 22_17174211_C_T 0 17174211 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2097
iter from getPCG1ofSigmaAndVector 1
AC 2977
S is 7.564482e-25
var1 is 2.317111e-10
p_exact 1
var2sparseGRM Here 2.317112e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2977
var1 2.317111e-10
var2null 2.317111e-10
var2null_noXadj 3.353139e-10
475 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3910 22 22_17510346_C_T 0 17510346 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3421
iter from getPCG1ofSigmaAndVector 1
AC 1382
S is 1.261635e-24
var1 is 1.396816e-10
p_exact 1
var2sparseGRM Here 1.396817e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1382
var1 1.396816e-10
var2null 1.396816e-10
var2null_noXadj 2.026389e-10
125 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
917 22 22_16906964_G_A 0 16906964 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3729
iter from getPCG1ofSigmaAndVector 1
AC 1099
S is 2.650068e-25
var1 is 1.198167e-10
p_exact 1
var2sparseGRM Here 1.198168e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1099
var1 1.198167e-10
var2null 1.198167e-10
var2null_noXadj 1.858969e-10
466 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 0 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3856 22 22_17499058_T_C 0 17499058 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2848
iter from getPCG1ofSigmaAndVector 1
AC 2355
S is 1.459885e-24
var1 is 2.27525e-10
p_exact 1
var2sparseGRM Here 2.275251e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2355
var1 2.27525e-10
var2null 2.27525e-10
var2null_noXadj 3.915373e-10
8 th marker in geno 1
MAC: 43
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 0 0 0 0 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
110 22 22_16594856_C_CT 0 16594856 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3119
iter from getPCG1ofSigmaAndVector 1
AC 1699
S is -2.203181e-24
var1 is 1.463611e-10
p_exact 1
var2sparseGRM Here 1.463612e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1699
var1 1.463611e-10
var2null 1.463611e-10
var2null_noXadj 2.332095e-10
244 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 1 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1952 22 22_17147758_C_T 0 17147758 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2625
iter from getPCG1ofSigmaAndVector 1
AC 2457
S is -7.982515e-25
var1 is 2.751918e-10
p_exact 1
var2sparseGRM Here 2.75192e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2457
var1 2.751918e-10
var2null 2.751918e-10
var2null_noXadj 3.462799e-10
223 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1787 22 22_17117420_C_T 0 17117420 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2799
iter from getPCG1ofSigmaAndVector 1
AC 2404
S is 8.6521e-25
var1 is 2.442336e-10
p_exact 1
var2sparseGRM Here 2.442337e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2404
var1 2.442336e-10
var2null 2.442336e-10
var2null_noXadj 3.977202e-10
95 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
704 22 22_16842702_G_A 0 16842702 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3816
iter from getPCG1ofSigmaAndVector 1
AC 1022
S is -4.525411e-25
var1 is 1.315691e-10
p_exact 1
var2sparseGRM Here 1.315691e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1022
var1 1.315691e-10
var2null 1.315691e-10
var2null_noXadj 2.030677e-10
198 th marker in geno 1
MAC: 96
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1627 22 22_17074025_G_A 0 17074025 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1652
iter from getPCG1ofSigmaAndVector 1
AC 4607
S is -2.003e-24
var1 is 3.557996e-10
p_exact 1
var2sparseGRM Here 3.557999e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4607
var1 3.557996e-10
var2null 3.557997e-10
var2null_noXadj 5.922073e-10
180 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1517 22 22_17046605_G_C 0 17046605 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1696
iter from getPCG1ofSigmaAndVector 1
AC 4563
S is -2.340809e-24
var1 is 3.541055e-10
p_exact 1
var2sparseGRM Here 3.541058e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4563
var1 3.541055e-10
var2null 3.541056e-10
var2null_noXadj 6.009567e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364
CV for variance ratio estimate using 50 markers is 0.002440275 > 0.001
try 60 markers
415 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3261 22 22_17408995_A_T 0 17408995 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 841
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 2.754601e-24
var1 is 2.020824e-10
p_exact 1
var2sparseGRM Here 2.020825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.020824e-10
var2null 2.020824e-10
var2null_noXadj 2.851867e-10
258 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2090 22 22_17170041_C_T 0 17170041 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1738
S is 8.149564e-25
var1 is 1.690214e-10
p_exact 1
var2sparseGRM Here 1.690214e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1738
var1 1.690214e-10
var2null 1.690214e-10
var2null_noXadj 2.678111e-10
189 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1556 22 22_17054364_T_C 0 17054364 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
31 th marker in geno 1
MAC: 61
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
269 22 22_16713436_T_C 0 16713436 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1649
iter from getPCG1ofSigmaAndVector 1
AC 3725
S is 1.456439e-24
var1 is 2.46971e-10
p_exact 1
var2sparseGRM Here 2.469712e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3725
var1 2.46971e-10
var2null 2.46971e-10
var2null_noXadj 4.049186e-10
105 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 0 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
774 22 22_16859187_A_G 0 16859187 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2565
iter from getPCG1ofSigmaAndVector 1
AC 2668
S is 1.219263e-26
var1 is 2.098046e-10
p_exact 1
var2sparseGRM Here 2.098047e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2668
var1 2.098046e-10
var2null 2.098046e-10
var2null_noXadj 4.084232e-10
284 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2265 22 22_17187678_A_G 0 17187678 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2620
iter from getPCG1ofSigmaAndVector 1
AC 2289
S is -3.581302e-24
var1 is 1.781993e-10
p_exact 1
var2sparseGRM Here 1.781994e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2289
var1 1.781993e-10
var2null 1.781993e-10
var2null_noXadj 2.897403e-10
383 th marker in geno 1
MAC: 25
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2917 22 22_17323505_T_C 0 17323505 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3926
iter from getPCG1ofSigmaAndVector 1
AC 953
S is 4.145874e-25
var1 is 1.143702e-10
p_exact 1
var2sparseGRM Here 1.143702e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 953
var1 1.143702e-10
var2null 1.143702e-10
var2null_noXadj 1.937254e-10
136 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 2 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
975 22 22_16924021_C_G 0 16924021 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1568
iter from getPCG1ofSigmaAndVector 1
AC 3811
S is -4.228698e-24
var1 is 2.946292e-10
p_exact 1
var2sparseGRM Here 2.946293e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3811
var1 2.946292e-10
var2null 2.946292e-10
var2null_noXadj 3.805914e-10
190 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1565 22 22_17055665_A_G 0 17055665 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
264 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2137 22 22_17174286_G_C 0 17174286 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1387
iter from getPCG1ofSigmaAndVector 1
AC 3709
S is 4.247151e-24
var1 is 1.671652e-10
p_exact 1
var2sparseGRM Here 1.671653e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3709
var1 1.671652e-10
var2null 1.671652e-10
var2null_noXadj 2.812566e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514
CV for variance ratio estimate using 60 markers is 0.00200029 > 0.001
try 70 markers
39 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
323 22 22_16733220_A_G 0 16733220 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3614
iter from getPCG1ofSigmaAndVector 1
AC 1214
S is 6.221904e-25
var1 is 1.265151e-10
p_exact 1
var2sparseGRM Here 1.265152e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1214
var1 1.265151e-10
var2null 1.265151e-10
var2null_noXadj 1.974943e-10
310 th marker in geno 1
MAC: 95
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 0 2 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2445 22 22_17216771_A_C 0 17216771 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1397
iter from getPCG1ofSigmaAndVector 1
AC 4055
S is -2.648907e-24
var1 is 2.07781e-10
p_exact 1
var2sparseGRM Here 2.077811e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4055
var1 2.07781e-10
var2null 2.07781e-10
var2null_noXadj 4.08645e-10
304 th marker in geno 1
MAC: 91
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 1 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2412 22 22_17211494_G_A 0 17211494 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1234
iter from getPCG1ofSigmaAndVector 1
AC 4628
S is -3.614876e-25
var1 is 2.535832e-10
p_exact 1
var2sparseGRM Here 2.535833e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4628
var1 2.535832e-10
var2null 2.535832e-10
var2null_noXadj 4.47393e-10
252 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2029 22 22_17160649_GA_G 0 17160649 GA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2982
iter from getPCG1ofSigmaAndVector 1
AC 2014
S is -1.064451e-24
var1 is 2.481048e-10
p_exact 1
var2sparseGRM Here 2.481049e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2014
var1 2.481048e-10
var2null 2.481048e-10
var2null_noXadj 3.179093e-10
397 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3059 22 22_17358468_C_T 0 17358468 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1408
iter from getPCG1ofSigmaAndVector 1
AC 4358
S is 5.205845e-24
var1 is 3.474116e-10
p_exact 1
var2sparseGRM Here 3.474119e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4358
var1 3.474116e-10
var2null 3.474116e-10
var2null_noXadj 4.480805e-10
393 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3045 22 22_17353687_T_C 0 17353687 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1392
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is 6.121056e-24
var1 is 3.073406e-10
p_exact 1
var2sparseGRM Here 3.073408e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 3.073406e-10
var2null 3.073406e-10
var2null_noXadj 4.9917e-10
428 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
3392 22 22_17427809_A_G 0 17427809 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3954
iter from getPCG1ofSigmaAndVector 1
AC 870
S is -5.028515e-26
var1 is 1.254682e-10
p_exact 1
var2sparseGRM Here 1.254682e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 870
var1 1.254682e-10
var2null 1.254682e-10
var2null_noXadj 1.620206e-10
417 th marker in geno 1
MAC: 88
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3298 22 22_17417019_CT_C 0 17417019 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1164
iter from getPCG1ofSigmaAndVector 1
AC 4331
S is 2.730797e-24
var1 is 2.440372e-10
p_exact 1
var2sparseGRM Here 2.440373e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4331
var1 2.440372e-10
var2null 2.440372e-10
var2null_noXadj 3.505081e-10
36 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
299 22 22_16724286_T_C 0 16724286 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3558
iter from getPCG1ofSigmaAndVector 1
AC 1270
S is 1.621254e-24
var1 is 1.295267e-10
p_exact 1
var2sparseGRM Here 1.295268e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1270
var1 1.295267e-10
var2null 1.295267e-10
var2null_noXadj 2.022097e-10
155 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1122 22 22_16958936_G_A 0 16958936 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
CV for variance ratio estimate using 70 markers is 0.001829244 > 0.001
try 80 markers
162 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1201 22 22_16975883_A_C 0 16975883 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
293 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2318 22 22_17196323_C_CA 0 17196323 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2536
iter from getPCG1ofSigmaAndVector 1
AC 2703
S is 2.721993e-24
var1 is 2.683981e-10
p_exact 1
var2sparseGRM Here 2.683983e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2703
var1 2.683981e-10
var2null 2.683981e-10
var2null_noXadj 4.028041e-10
27 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
246 22 22_16705760_TA_T 0 16705760 TA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1691
iter from getPCG1ofSigmaAndVector 1
AC 3683
S is 1.564128e-24
var1 is 2.576679e-10
p_exact 1
var2sparseGRM Here 2.57668e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3683
var1 2.576679e-10
var2null 2.576679e-10
var2null_noXadj 4.096401e-10
58 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
477 22 22_16788186_C_T 0 16788186 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2719
iter from getPCG1ofSigmaAndVector 1
AC 2037
S is -2.836113e-24
var1 is 1.381818e-10
p_exact 1
var2sparseGRM Here 1.381819e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2037
var1 1.381818e-10
var2null 1.381819e-10
var2null_noXadj 2.274347e-10
48 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 1 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
384 22 22_16747765_CT_C 0 16747765 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2030
iter from getPCG1ofSigmaAndVector 1
AC 3386
S is -4.638452e-24
var1 is 2.792877e-10
p_exact 1
var2sparseGRM Here 2.792879e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3386
var1 2.792877e-10
var2null 2.792878e-10
var2null_noXadj 4.518904e-10
127 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
930 22 22_16908129_T_A 0 16908129 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3729
iter from getPCG1ofSigmaAndVector 1
AC 1099
S is 2.650068e-25
var1 is 1.198167e-10
p_exact 1
var2sparseGRM Here 1.198168e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1099
var1 1.198167e-10
var2null 1.198167e-10
var2null_noXadj 1.858969e-10
367 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2842 22 22_17307364_G_A 0 17307364 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2066
iter from getPCG1ofSigmaAndVector 1
AC 3397
S is 1.83874e-24
var1 is 2.369872e-10
p_exact 1
var2sparseGRM Here 2.369873e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3397
var1 2.369872e-10
var2null 2.369872e-10
var2null_noXadj 4.480572e-10
123 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
886 22 22_16886615_AT_A 0 16886615 AT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3843
iter from getPCG1ofSigmaAndVector 1
AC 1057
S is 4.325735e-25
var1 is 1.35786e-10
p_exact 1
var2sparseGRM Here 1.35786e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1057
var1 1.35786e-10
var2null 1.35786e-10
var2null_noXadj 2.085715e-10
94 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
686 22 22_16839591_T_C 0 16839591 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3894
iter from getPCG1ofSigmaAndVector 1
AC 944
S is -6.908465e-25
var1 is 1.240043e-10
p_exact 1
var2sparseGRM Here 1.240043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 944
var1 1.240043e-10
var2null 1.240043e-10
var2null_noXadj 1.861653e-10
279 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2242 22 22_17184523_T_C 0 17184523 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3571
iter from getPCG1ofSigmaAndVector 1
AC 1297
S is -2.184577e-25
var1 is 9.989261e-11
p_exact 1
var2sparseGRM Here 9.989264e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1297
var1 9.989261e-11
var2null 9.989262e-11
var2null_noXadj 2.193226e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597
CV for variance ratio estimate using 80 markers is 0.001610003 > 0.001
try 90 markers
236 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 1 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1864 22 22_17131854_G_A 0 17131854 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2639
iter from getPCG1ofSigmaAndVector 1
AC 2712
S is -3.435647e-26
var1 is 2.77587e-10
p_exact 1
var2sparseGRM Here 2.775872e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2712
var1 2.77587e-10
var2null 2.77587e-10
var2null_noXadj 4.515445e-10
450 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3566 22 22_17448910_C_T 0 17448910 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
166 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1369 22 22_17014255_C_T 0 17014255 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3405
iter from getPCG1ofSigmaAndVector 1
AC 1467
S is 2.641359e-25
var1 is 1.654633e-10
p_exact 1
var2sparseGRM Here 1.654634e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1467
var1 1.654633e-10
var2null 1.654633e-10
var2null_noXadj 2.343161e-10
413 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3251 22 22_17406562_G_A 0 17406562 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 841
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 2.754601e-24
var1 is 2.020824e-10
p_exact 1
var2sparseGRM Here 2.020825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.020824e-10
var2null 2.020824e-10
var2null_noXadj 2.851867e-10
68 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
543 22 22_16806309_C_CAT 0 16806309 C CAT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3625
iter from getPCG1ofSigmaAndVector 1
AC 1143
S is 2.171955e-25
var1 is 1.083828e-10
p_exact 1
var2sparseGRM Here 1.083828e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1143
var1 1.083828e-10
var2null 1.083828e-10
var2null_noXadj 1.679953e-10
276 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 1 1 1 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2207 22 22_17179611_C_G 0 17179611 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1048
iter from getPCG1ofSigmaAndVector 1
AC 4169
S is 1.606348e-24
var1 is 1.968281e-10
p_exact 1
var2sparseGRM Here 1.968281e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4169
var1 1.968281e-10
var2null 1.968281e-10
var2null_noXadj 2.751443e-10
25 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 0 0 0 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
226 22 22_16697442_G_T 0 16697442 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 995
iter from getPCG1ofSigmaAndVector 1
AC 4722
S is 4.25405e-24
var1 is 2.405499e-10
p_exact 1
var2sparseGRM Here 2.4055e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4722
var1 2.405499e-10
var2null 2.405499e-10
var2null_noXadj 3.868031e-10
182 th marker in geno 1
MAC: 34
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1525 22 22_17049480_A_G 0 17049480 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3708
iter from getPCG1ofSigmaAndVector 1
AC 1083
S is 1.803904e-25
var1 is 9.715818e-11
p_exact 1
var2sparseGRM Here 9.715822e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1083
var1 9.715818e-11
var2null 9.715819e-11
var2null_noXadj 1.81562e-10
175 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1479 22 22_17037865_G_T 0 17037865 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
85 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
629 22 22_16825380_G_A 0 16825380 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2017
iter from getPCG1ofSigmaAndVector 1
AC 3372
S is -1.03857e-24
var1 is 2.609921e-10
p_exact 1
var2sparseGRM Here 2.609921e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3372
var1 2.609921e-10
var2null 2.609921e-10
var2null_noXadj 4.353054e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609
CV for variance ratio estimate using 90 markers is 0.001388658 > 0.001
try 100 markers
57 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
470 22 22_16785735_A_C 0 16785735 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
86 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
630 22 22_16826051_T_TAAC 0 16826051 T TAAC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1281
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 3.209919e-24
var1 is 2.792824e-10
p_exact 1
var2sparseGRM Here 2.792825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.792824e-10
var2null 2.792825e-10
var2null_noXadj 4.687222e-10
482 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3961 22 22_17519297_T_G 0 17519297 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
205 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1706 22 22_17100141_TAA_T 0 17100141 TAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3757
iter from getPCG1ofSigmaAndVector 1
AC 1067
S is 3.586525e-25
var1 is 1.225337e-10
p_exact 1
var2sparseGRM Here 1.225338e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1067
var1 1.225337e-10
var2null 1.225337e-10
var2null_noXadj 1.810654e-10
240 th marker in geno 1
MAC: 65
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 2 1 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
1915 22 22_17137274_C_G 0 17137274 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2388
iter from getPCG1ofSigmaAndVector 1
AC 2572
S is 2.21545e-24
var1 is 1.940903e-10
p_exact 1
var2sparseGRM Here 1.940903e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2572
var1 1.940903e-10
var2null 1.940903e-10
var2null_noXadj 3.092207e-10
148 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1078 22 22_16947190_T_C 0 16947190 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1816
iter from getPCG1ofSigmaAndVector 1
AC 3745
S is -4.252755e-24
var1 is 2.582015e-10
p_exact 1
var2sparseGRM Here 2.582015e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3745
var1 2.582015e-10
var2null 2.582015e-10
var2null_noXadj 4.689406e-10
484 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3973 22 22_17521351_T_A 0 17521351 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
141 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 1 0 2 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1005 22 22_16931326_A_G 0 16931326 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2126
iter from getPCG1ofSigmaAndVector 1
AC 3016
S is -2.314631e-24
var1 is 2.449201e-10
p_exact 1
var2sparseGRM Here 2.449202e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3016
var1 2.449201e-10
var2null 2.449201e-10
var2null_noXadj 3.529569e-10
56 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
457 22 22_16781299_C_T 0 16781299 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
363 th marker in geno 1
MAC: 89
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2808 22 22_17303033_G_A 0 17303033 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1463
iter from getPCG1ofSigmaAndVector 1
AC 4385
S is -4.3843e-25
var1 is 2.645537e-10
p_exact 1
var2sparseGRM Here 2.645538e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4385
var1 2.645537e-10
var2null 2.645537e-10
var2null_noXadj 4.747337e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676
CV for variance ratio estimate using 100 markers is 0.001248106 > 0.001
try 110 markers
91 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
671 22 22_16836343_A_C 0 16836343 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3657
iter from getPCG1ofSigmaAndVector 1
AC 1369
S is 3.350702e-25
var1 is 2.058348e-10
p_exact 1
var2sparseGRM Here 2.058349e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1369
var1 2.058348e-10
var2null 2.058348e-10
var2null_noXadj 2.979653e-10
344 th marker in geno 1
MAC: 29
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2642 22 22_17250567_T_TAAAATAA 0 17250567 T TAAAATAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3561
iter from getPCG1ofSigmaAndVector 1
AC 1293
S is -5.852391e-25
var1 is 1.357912e-10
p_exact 1
var2sparseGRM Here 1.357912e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1293
var1 1.357912e-10
var2null 1.357912e-10
var2null_noXadj 2.144203e-10
253 th marker in geno 1
MAC: 48
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2036 22 22_17161022_A_G 0 17161022 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2814
iter from getPCG1ofSigmaAndVector 1
AC 2574
S is -3.580696e-24
var1 is 3.388007e-10
p_exact 1
var2sparseGRM Here 3.388009e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2574
var1 3.388007e-10
var2null 3.388007e-10
var2null_noXadj 4.617044e-10
322 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2485 22 22_17221690_T_C 0 17221690 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2859
iter from getPCG1ofSigmaAndVector 1
AC 2810
S is 5.546513e-25
var1 is 2.895086e-10
p_exact 1
var2sparseGRM Here 2.895089e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2810
var1 2.895086e-10
var2null 2.895087e-10
var2null_noXadj 5.988163e-10
438 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3507 22 22_17441603_A_AC 0 17441603 A AC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
518 th marker in geno 1
MAC: 77
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4231 22 22_17572793_C_T 0 17572793 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2124
iter from getPCG1ofSigmaAndVector 1
AC 3558
S is -4.092535e-24
var1 is 3.015379e-10
p_exact 1
var2sparseGRM Here 3.01538e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3558
var1 3.015379e-10
var2null 3.015379e-10
var2null_noXadj 5.179161e-10
52 th marker in geno 1
MAC: 51
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
449 22 22_16769333_T_C 0 16769333 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2289
iter from getPCG1ofSigmaAndVector 1
AC 2731
S is -7.096214e-25
var1 is 2.152456e-10
p_exact 1
var2sparseGRM Here 2.152457e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2731
var1 2.152456e-10
var2null 2.152456e-10
var2null_noXadj 3.225962e-10
195 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1607 22 22_17066270_C_A 0 17066270 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2952
iter from getPCG1ofSigmaAndVector 1
AC 2155
S is -1.796378e-24
var1 is 2.287538e-10
p_exact 1
var2sparseGRM Here 2.287539e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2155
var1 2.287538e-10
var2null 2.287538e-10
var2null_noXadj 3.594958e-10
504 th marker in geno 1
MAC: 82
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
4156 22 22_17556556_G_A 0 17556556 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1761
iter from getPCG1ofSigmaAndVector 1
AC 4013
S is 6.219506e-25
var1 is 2.765841e-10
p_exact 1
var2sparseGRM Here 2.765843e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4013
var1 2.765841e-10
var2null 2.765842e-10
var2null_noXadj 5.008253e-10
204 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 1 2 1 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1685 22 22_17092382_A_G 0 17092382 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1299
iter from getPCG1ofSigmaAndVector 1
AC 4568
S is -4.213742e-24
var1 is 2.015821e-10
p_exact 1
var2sparseGRM Here 2.015822e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4568
var1 2.015821e-10
var2null 2.015821e-10
var2null_noXadj 4.535953e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096
CV for variance ratio estimate using 110 markers is 0.001151453 > 0.001
try 120 markers
515 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
4216 22 22_17570663_A_G 0 17570663 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2428
iter from getPCG1ofSigmaAndVector 1
AC 2762
S is -4.176293e-24
var1 is 1.689767e-10
p_exact 1
var2sparseGRM Here 1.689768e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2762
var1 1.689767e-10
var2null 1.689767e-10
var2null_noXadj 3.839481e-10
44 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
362 22 22_16743136_G_A 0 16743136 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1778
S is -5.863572e-25
var1 is 2.020268e-10
p_exact 1
var2sparseGRM Here 2.02027e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1778
var1 2.020268e-10
var2null 2.020268e-10
var2null_noXadj 2.794007e-10
286 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 2 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2276 22 22_17188516_G_C 0 17188516 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2273
iter from getPCG1ofSigmaAndVector 1
AC 3373
S is -3.717466e-24
var1 is 2.827461e-10
p_exact 1
var2sparseGRM Here 2.827462e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3373
var1 2.827461e-10
var2null 2.827461e-10
var2null_noXadj 5.229961e-10
213 th marker in geno 1
MAC: 63
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
1732 22 22_17106856_GGGC_G 0 17106856 GGGC G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2864
iter from getPCG1ofSigmaAndVector 1
AC 2181
S is -1.956375e-25
var1 is 2.37367e-10
p_exact 1
var2sparseGRM Here 2.373671e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2181
var1 2.37367e-10
var2null 2.37367e-10
var2null_noXadj 3.631997e-10
93 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
681 22 22_16839471_A_T 0 16839471 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1534
iter from getPCG1ofSigmaAndVector 1
AC 3866
S is -1.413437e-24
var1 is 2.545011e-10
p_exact 1
var2sparseGRM Here 2.545012e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3866
var1 2.545011e-10
var2null 2.545011e-10
var2null_noXadj 3.785768e-10
59 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
481 22 22_16790535_G_A 0 16790535 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
256 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2062 22 22_17166972_T_G 0 17166972 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3155
iter from getPCG1ofSigmaAndVector 1
AC 2155
S is -9.513726e-25
var1 is 2.926539e-10
p_exact 1
var2sparseGRM Here 2.926541e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2155
var1 2.926539e-10
var2null 2.92654e-10
var2null_noXadj 4.305838e-10
346 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2657 22 22_17251532_C_CA 0 17251532 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3278
iter from getPCG1ofSigmaAndVector 1
AC 1612
S is -4.940163e-25
var1 is 1.79778e-10
p_exact 1
var2sparseGRM Here 1.797781e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1612
var1 1.79778e-10
var2null 1.79778e-10
var2null_noXadj 2.506762e-10
335 th marker in geno 1
MAC: 66
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 0 1 1 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
2588 22 22_17243159_C_A 0 17243159 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2308
iter from getPCG1ofSigmaAndVector 1
AC 2896
S is -1.710023e-24
var1 is 2.438792e-10
p_exact 1
var2sparseGRM Here 2.438794e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2896
var1 2.438792e-10
var2null 2.438792e-10
var2null_noXadj 3.856526e-10
109 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
801 22 22_16864232_G_A 0 16864232 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3653
iter from getPCG1ofSigmaAndVector 1
AC 1185
S is -7.237325e-26
var1 is 1.148315e-10
p_exact 1
var2sparseGRM Here 1.148315e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1185
var1 1.148315e-10
var2null 1.148315e-10
var2null_noXadj 2.012894e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[120] 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096 0.4401030 0.7230721
[113] 0.5406275 0.6535440 0.6722575 0.6035108 0.6796677 0.7171722 0.6323806
[120] 0.5704797
CV for variance ratio estimate using 120 markers is 0.001060431 > 0.001
try 130 markers
442 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3521 22 22_17443691_C_T 0 17443691 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
203 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 2 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1679 22 22_17090465_G_A 0 17090465 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2267
iter from getPCG1ofSigmaAndVector 1
AC 3285
S is -2.134393e-24
var1 is 3.340378e-10
p_exact 1
var2sparseGRM Here 3.34038e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3285
var1 3.340378e-10
var2null 3.340378e-10
var2null_noXadj 4.901084e-10
392 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3032 22 22_17352210_T_C 0 17352210 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1392
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is 6.121056e-24
var1 is 3.073406e-10
p_exact 1
var2sparseGRM Here 3.073408e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 3.073406e-10
var2null 3.073406e-10
var2null_noXadj 4.9917e-10
294 th marker in geno 1
MAC: 98
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 2 2 1 2 1 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2319 22 22_17196809_C_T 0 17196809 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1757
iter from getPCG1ofSigmaAndVector 1
AC 3747
S is 8.885729e-27
var1 is 2.204993e-10
p_exact 1
var2sparseGRM Here 2.204995e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3747
var1 2.204993e-10
var2null 2.204993e-10
var2null_noXadj 4.569122e-10
154 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1100 22 22_16954034_G_C 0 16954034 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2286
iter from getPCG1ofSigmaAndVector 1
AC 2716
S is -6.334364e-25
var1 is 1.815757e-10
p_exact 1
var2sparseGRM Here 1.815757e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2716
var1 1.815757e-10
var2null 1.815757e-10
var2null_noXadj 3.117158e-10
80 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
612 22 22_16822150_T_C 0 16822150 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2017
iter from getPCG1ofSigmaAndVector 1
AC 3372
S is -1.03857e-24
var1 is 2.609921e-10
p_exact 1
var2sparseGRM Here 2.609921e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3372
var1 2.609921e-10
var2null 2.609921e-10
var2null_noXadj 4.353054e-10
243 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1948 22 22_17145775_T_C 0 17145775 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3327
iter from getPCG1ofSigmaAndVector 1
AC 1541
S is 1.019234e-24
var1 is 1.184986e-10
p_exact 1
var2sparseGRM Here 1.184987e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1541
var1 1.184986e-10
var2null 1.184987e-10
var2null_noXadj 2.378183e-10
296 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2323 22 22_17197269_C_CT 0 17197269 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3249
iter from getPCG1ofSigmaAndVector 1
AC 1605
S is -1.804802e-24
var1 is 1.691563e-10
p_exact 1
var2sparseGRM Here 1.691565e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1605
var1 1.691563e-10
var2null 1.691564e-10
var2null_noXadj 2.386271e-10
35 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
294 22 22_16724268_T_C 0 16724268 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3558
iter from getPCG1ofSigmaAndVector 1
AC 1270
S is 1.621254e-24
var1 is 1.295267e-10
p_exact 1
var2sparseGRM Here 1.295268e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1270
var1 1.295267e-10
var2null 1.295267e-10
var2null_noXadj 2.022097e-10
100 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
743 22 22_16851949_G_A 0 16851949 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1548
iter from getPCG1ofSigmaAndVector 1
AC 3852
S is -1.19253e-24
var1 is 2.561159e-10
p_exact 1
var2sparseGRM Here 2.561161e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3852
var1 2.561159e-10
var2null 2.561159e-10
var2null_noXadj 3.799173e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[120] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[127] 0.9999997 1.0000000 1.0000000 0.9999998
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096 0.4401030 0.7230721
[113] 0.5406275 0.6535440 0.6722575 0.6035108 0.6796677 0.7171722 0.6323806
[120] 0.5704797 0.6053607 0.6815590 0.6157032 0.4825858 0.5825038 0.5995609
[127] 0.4982739 0.7088730 0.6405563 0.6741359
CV for variance ratio estimate using 130 markers is 0.0009729458 < 0.001
varRatio_sparseGRM_vec
[1] 0.9999991 0.9999992 0.9999992 0.9999996 0.9999997 0.9999996 0.9999993
[8] 0.9999996 0.9999996 0.9999994 0.9999994 0.9999992 0.9999997 0.9999996
[15] 0.9999996 0.9999997 0.9999997 0.9999995 0.9999995 0.9999998 0.9999997
[22] 0.9999997 0.9999998 0.9999995 0.9999993 0.9999998 0.9999995 0.9999993
[29] 0.9999995 0.9999996 0.9999996 0.9999990 0.9999995 0.9999996 0.9999999
[36] 0.9999994 0.9999996 0.9999995 0.9999994 0.9999995 0.9999998 0.9999997
[43] 0.9999996 0.9999995 0.9999995 0.9999992 0.9999998 0.9999997 0.9999994
[50] 0.9999994 0.9999995 0.9999998 0.9999996 0.9999993 0.9999993 0.9999996
[57] 0.9999999 0.9999996 0.9999996 0.9999998 0.9999995 0.9999997 0.9999995
[64] 0.9999995 0.9999991 0.9999991 1.0000000 0.9999996 0.9999995 0.9999996
[71] 0.9999996 0.9999990 0.9999995 0.9999992 0.9999993 0.9999996 0.9999997
[78] 0.9999999 0.9999998 0.9999997 0.9999994 0.9999995 0.9999994 0.9999995
[85] 0.9999994 0.9999999 0.9999994 0.9999996 0.9999996 0.9999999 0.9999994
[92] 0.9999995 0.9999996 0.9999998 0.9999998 0.9999997 0.9999996 0.9999995
[99] 0.9999994 0.9999997 0.9999995 0.9999995 0.9999993 0.9999990 0.9999995
[106] 0.9999996 0.9999995 0.9999995 0.9999995 0.9999996 0.9999996 0.9999992
[113] 0.9999996 0.9999997 0.9999994 0.9999994 0.9999994 0.9999996 0.9999993
[120] 0.9999998 0.9999995 0.9999993 0.9999991 0.9999993 0.9999995 0.9999999
[127] 0.9999993 0.9999993 0.9999995 0.9999992
varRatio_sparse 0.9999995
varRatio_null 0.9999999
varRatio_null_noXadj 0.6178561
V1 V2 V3
1 0.9999995 sparse 1
2 0.9999999 null 1
3 0.6178561 null_noXadj 1
4 0.9999999 null_sample 1
[2026-01-09 01:39:49,463] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: optparse
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: RhpcBLASctl
warning: solve(): system is singular; attempting approx solution
Loading required package: fastSave
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
3: glm.fit: algorithm did not converge
[2026-01-09 01:39:49,466] INFO:cellink.tl.external._saigeqtl: Running Step 2: Association tests
[2026-01-09 01:39:49,467] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step2_tests_qtl.R --bedFile=saigeqtl_complete.bed --bimFile=saigeqtl_complete.bim --famFile=saigeqtl_complete.fam --GMMATmodelFile=saigeqtl_complete.rda --varianceRatioFile=saigeqtl_complete.varianceRatio.txt --SAIGEOutputFile=saigeqtl_complete_results.txt --minMAC=20 --LOCO=FALSE --rangestoIncludeFile=saigeqtl_complete_ranges.txt
[2026-01-09 01:40:05,771] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.17.6 optparse_1.7.5 RhpcBLASctl_0.23-42
[4] SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] RcppParallel_5.1.9 lattice_0.22-7
$vcfFile
[1] ""
$vcfFileIndex
[1] ""
$vcfField
[1] "DS"
$savFile
[1] ""
$savFileIndex
[1] ""
$bgenFile
[1] ""
$bgenFileIndex
[1] ""
$sampleFile
[1] ""
$bedFile
[1] "saigeqtl_complete.bed"
$bimFile
[1] "saigeqtl_complete.bim"
$famFile
[1] "saigeqtl_complete.fam"
$AlleleOrder
[1] "alt-first"
$idstoIncludeFile
[1] ""
$rangestoIncludeFile
[1] "saigeqtl_complete_ranges.txt"
$chrom
[1] ""
$is_imputed_data
[1] FALSE
$minMAF
[1] 0
$minMAC
[1] 20
$minGroupMAC_in_BurdenTest
[1] 5
$minInfo
[1] 0
$maxMissing
[1] 0.15
$impute_method
[1] "best_guess"
$LOCO
[1] FALSE
$GMMATmodelFile
[1] "saigeqtl_complete.rda"
$varianceRatioFile
[1] "saigeqtl_complete.varianceRatio.txt"
$GMMATmodel_varianceRatio_multiTraits_File
[1] ""
$SAIGEOutputFile
[1] "saigeqtl_complete_results.txt"
$markers_per_chunk
[1] 10000
$groups_per_chunk
[1] 100
$is_output_moreDetails
[1] FALSE
$is_overwrite_output
[1] TRUE
$maxMAF_in_groupTest
[1] "0.0001,0.001,0.01"
$maxMAC_in_groupTest
[1] "0"
$annotation_in_groupTest
[1] "lof,missense;lof,missense;lof;synonymous"
$groupFile
[1] ""
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$relatednessCutoff
[1] 0
$MACCutoff_to_CollapseUltraRare
[1] 10
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$weights.beta
[1] "1;25"
$r.corr
[1] 0
$markers_per_chunk_in_groupTest
[1] 100
$condition
[1] ""
$SPAcutoff
[1] 2
$dosage_zerod_cutoff
[1] 0.2
$dosage_zerod_MAC_cutoff
[1] 10
$is_single_in_groupTest
[1] FALSE
$is_SKATO
[1] FALSE
$is_equal_weight_in_groupTest
[1] FALSE
$is_output_markerList_in_groupTest
[1] FALSE
$is_Firth_beta
[1] FALSE
$pCutoffforFirth
[1] 0.01
$is_fastTest
[1] FALSE
$is_noadjCov
[1] TRUE
$is_sparseGRM
[1] FALSE
$pval_cutoff_for_fastTest
[1] 0.05
$max_MAC_for_ER
[1] 4
$is_EmpSPA
[1] FALSE
$help
[1] FALSE
[1] "opt$r.corr"
[1] 0
dosage_zerod_cutoff 0.2
Any dosages <= 0.2 for genetic variants with MAC <= 10 are set to be 0 in group tests
single-variant association test will be performed
[1] "Leave-one-chromosome-out is not applied"
[1] "LOCO = FASLE and leave-one-chromosome-out is not applied"
isSparseGRM FALSE
variance Ratio null is 0.9999999
variance Ratio null_noXadj is 0.6178561
variance Ratio ratioVec_null_sample is 0.9999999
$ratioVec_sparse
[1] 0.9999995
$ratioVec_null
[1] 0.9999999
$ratioVec_null_sample
[1] 0.9999999
$ratioVec_null_noXadj
[1] 0.6178561
$ratioVec_null_eg
[1] -1
$ratioVec_sparse_eg
[1] -1
dosageFile type is plink
allele order in the plink file is alt-first .
Reading bim file....
Reading fam file....
Setting position of samples in PLINK files....
871 ranges are in rangestoIncludeFile
22 markers in the range 1 are found in the geno/dosage file.
1422 markers in the range 2 are found in the geno/dosage file.
1686 markers in the range 3 are found in the geno/dosage file.
1705 markers in the range 4 are found in the geno/dosage file.
1784 markers in the range 5 are found in the geno/dosage file.
2156 markers in the range 6 are found in the geno/dosage file.
2627 markers in the range 7 are found in the geno/dosage file.
2632 markers in the range 8 are found in the geno/dosage file.
2931 markers in the range 9 are found in the geno/dosage file.
3109 markers in the range 10 are found in the geno/dosage file.
3224 markers in the range 11 are found in the geno/dosage file.
3270 markers in the range 12 are found in the geno/dosage file.
3312 markers in the range 13 are found in the geno/dosage file.
3350 markers in the range 14 are found in the geno/dosage file.
3433 markers in the range 15 are found in the geno/dosage file.
3880 markers in the range 16 are found in the geno/dosage file.
4200 markers in the range 17 are found in the geno/dosage file.
4194 markers in the range 18 are found in the geno/dosage file.
4151 markers in the range 19 are found in the geno/dosage file.
4151 markers in the range 20 are found in the geno/dosage file.
4147 markers in the range 21 are found in the geno/dosage file.
4128 markers in the range 22 are found in the geno/dosage file.
4112 markers in the range 23 are found in the geno/dosage file.
3865 markers in the range 24 are found in the geno/dosage file.
3498 markers in the range 25 are found in the geno/dosage file.
2883 markers in the range 26 are found in the geno/dosage file.
2677 markers in the range 27 are found in the geno/dosage file.
2638 markers in the range 28 are found in the geno/dosage file.
2593 markers in the range 29 are found in the geno/dosage file.
2437 markers in the range 30 are found in the geno/dosage file.
1734 markers in the range 31 are found in the geno/dosage file.
1532 markers in the range 32 are found in the geno/dosage file.
1501 markers in the range 33 are found in the geno/dosage file.
1484 markers in the range 34 are found in the geno/dosage file.
492 markers in the range 35 are found in the geno/dosage file.
395 markers in the range 36 are found in the geno/dosage file.
256 markers in the range 37 are found in the geno/dosage file.
33 markers in the range 38 are found in the geno/dosage file.
17 markers in the range 39 are found in the geno/dosage file.
0 markers in the range 40 are found in the geno/dosage file.
0 markers in the range 41 are found in the geno/dosage file.
0 markers in the range 42 are found in the geno/dosage file.
0 markers in the range 43 are found in the geno/dosage file.
0 markers in the range 44 are found in the geno/dosage file.
0 markers in the range 45 are found in the geno/dosage file.
0 markers in the range 46 are found in the geno/dosage file.
0 markers in the range 47 are found in the geno/dosage file.
0 markers in the range 48 are found in the geno/dosage file.
0 markers in the range 49 are found in the geno/dosage file.
0 markers in the range 50 are found in the geno/dosage file.
0 markers in the range 51 are found in the geno/dosage file.
0 markers in the range 52 are found in the geno/dosage file.
0 markers in the range 53 are found in the geno/dosage file.
0 markers in the range 54 are found in the geno/dosage file.
0 markers in the range 55 are found in the geno/dosage file.
0 markers in the range 56 are found in the geno/dosage file.
0 markers in the range 57 are found in the geno/dosage file.
0 markers in the range 58 are found in the geno/dosage file.
0 markers in the range 59 are found in the geno/dosage file.
0 markers in the range 60 are found in the geno/dosage file.
0 markers in the range 61 are found in the geno/dosage file.
0 markers in the range 62 are found in the geno/dosage file.
0 markers in the range 63 are found in the geno/dosage file.
0 markers in the range 64 are found in the geno/dosage file.
0 markers in the range 65 are found in the geno/dosage file.
0 markers in the range 66 are found in the geno/dosage file.
0 markers in the range 67 are found in the geno/dosage file.
0 markers in the range 68 are found in the geno/dosage file.
0 markers in the range 69 are found in the geno/dosage file.
0 markers in the range 70 are found in the geno/dosage file.
0 markers in the range 71 are found in the geno/dosage file.
0 markers in the range 72 are found in the geno/dosage file.
0 markers in the range 73 are found in the geno/dosage file.
0 markers in the range 74 are found in the geno/dosage file.
0 markers in the range 75 are found in the geno/dosage file.
0 markers in the range 76 are found in the geno/dosage file.
0 markers in the range 77 are found in the geno/dosage file.
0 markers in the range 78 are found in the geno/dosage file.
0 markers in the range 79 are found in the geno/dosage file.
0 markers in the range 80 are found in the geno/dosage file.
0 markers in the range 81 are found in the geno/dosage file.
0 markers in the range 82 are found in the geno/dosage file.
0 markers in the range 83 are found in the geno/dosage file.
0 markers in the range 84 are found in the geno/dosage file.
0 markers in the range 85 are found in the geno/dosage file.
0 markers in the range 86 are found in the geno/dosage file.
0 markers in the range 87 are found in the geno/dosage file.
0 markers in the range 88 are found in the geno/dosage file.
0 markers in the range 89 are found in the geno/dosage file.
0 markers in the range 90 are found in the geno/dosage file.
0 markers in the range 91 are found in the geno/dosage file.
0 markers in the range 92 are found in the geno/dosage file.
0 markers in the range 93 are found in the geno/dosage file.
0 markers in the range 94 are found in the geno/dosage file.
0 markers in the range 95 are found in the geno/dosage file.
0 markers in the range 96 are found in the geno/dosage file.
0 markers in the range 97 are found in the geno/dosage file.
0 markers in the range 98 are found in the geno/dosage file.
0 markers in the range 99 are found in the geno/dosage file.
0 markers in the range 100 are found in the geno/dosage file.
0 markers in the range 101 are found in the geno/dosage file.
0 markers in the range 102 are found in the geno/dosage file.
0 markers in the range 103 are found in the geno/dosage file.
0 markers in the range 104 are found in the geno/dosage file.
0 markers in the range 105 are found in the geno/dosage file.
0 markers in the range 106 are found in the geno/dosage file.
0 markers in the range 107 are found in the geno/dosage file.
0 markers in the range 108 are found in the geno/dosage file.
0 markers in the range 109 are found in the geno/dosage file.
0 markers in the range 110 are found in the geno/dosage file.
0 markers in the range 111 are found in the geno/dosage file.
0 markers in the range 112 are found in the geno/dosage file.
0 markers in the range 113 are found in the geno/dosage file.
0 markers in the range 114 are found in the geno/dosage file.
0 markers in the range 115 are found in the geno/dosage file.
0 markers in the range 116 are found in the geno/dosage file.
0 markers in the range 117 are found in the geno/dosage file.
0 markers in the range 118 are found in the geno/dosage file.
0 markers in the range 119 are found in the geno/dosage file.
0 markers in the range 120 are found in the geno/dosage file.
0 markers in the range 121 are found in the geno/dosage file.
0 markers in the range 122 are found in the geno/dosage file.
0 markers in the range 123 are found in the geno/dosage file.
0 markers in the range 124 are found in the geno/dosage file.
0 markers in the range 125 are found in the geno/dosage file.
0 markers in the range 126 are found in the geno/dosage file.
0 markers in the range 127 are found in the geno/dosage file.
0 markers in the range 128 are found in the geno/dosage file.
0 markers in the range 129 are found in the geno/dosage file.
0 markers in the range 130 are found in the geno/dosage file.
0 markers in the range 131 are found in the geno/dosage file.
0 markers in the range 132 are found in the geno/dosage file.
0 markers in the range 133 are found in the geno/dosage file.
0 markers in the range 134 are found in the geno/dosage file.
0 markers in the range 135 are found in the geno/dosage file.
0 markers in the range 136 are found in the geno/dosage file.
0 markers in the range 137 are found in the geno/dosage file.
0 markers in the range 138 are found in the geno/dosage file.
0 markers in the range 139 are found in the geno/dosage file.
0 markers in the range 140 are found in the geno/dosage file.
0 markers in the range 141 are found in the geno/dosage file.
0 markers in the range 142 are found in the geno/dosage file.
0 markers in the range 143 are found in the geno/dosage file.
0 markers in the range 144 are found in the geno/dosage file.
0 markers in the range 145 are found in the geno/dosage file.
0 markers in the range 146 are found in the geno/dosage file.
0 markers in the range 147 are found in the geno/dosage file.
0 markers in the range 148 are found in the geno/dosage file.
0 markers in the range 149 are found in the geno/dosage file.
0 markers in the range 150 are found in the geno/dosage file.
0 markers in the range 151 are found in the geno/dosage file.
0 markers in the range 152 are found in the geno/dosage file.
0 markers in the range 153 are found in the geno/dosage file.
0 markers in the range 154 are found in the geno/dosage file.
0 markers in the range 155 are found in the geno/dosage file.
0 markers in the range 156 are found in the geno/dosage file.
0 markers in the range 157 are found in the geno/dosage file.
0 markers in the range 158 are found in the geno/dosage file.
0 markers in the range 159 are found in the geno/dosage file.
0 markers in the range 160 are found in the geno/dosage file.
0 markers in the range 161 are found in the geno/dosage file.
0 markers in the range 162 are found in the geno/dosage file.
0 markers in the range 163 are found in the geno/dosage file.
0 markers in the range 164 are found in the geno/dosage file.
0 markers in the range 165 are found in the geno/dosage file.
0 markers in the range 166 are found in the geno/dosage file.
0 markers in the range 167 are found in the geno/dosage file.
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0 markers in the range 594 are found in the geno/dosage file.
0 markers in the range 595 are found in the geno/dosage file.
0 markers in the range 596 are found in the geno/dosage file.
0 markers in the range 597 are found in the geno/dosage file.
0 markers in the range 598 are found in the geno/dosage file.
0 markers in the range 599 are found in the geno/dosage file.
0 markers in the range 600 are found in the geno/dosage file.
0 markers in the range 601 are found in the geno/dosage file.
0 markers in the range 602 are found in the geno/dosage file.
0 markers in the range 603 are found in the geno/dosage file.
0 markers in the range 604 are found in the geno/dosage file.
0 markers in the range 605 are found in the geno/dosage file.
0 markers in the range 606 are found in the geno/dosage file.
0 markers in the range 607 are found in the geno/dosage file.
0 markers in the range 608 are found in the geno/dosage file.
0 markers in the range 609 are found in the geno/dosage file.
0 markers in the range 610 are found in the geno/dosage file.
0 markers in the range 611 are found in the geno/dosage file.
0 markers in the range 612 are found in the geno/dosage file.
0 markers in the range 613 are found in the geno/dosage file.
0 markers in the range 614 are found in the geno/dosage file.
0 markers in the range 615 are found in the geno/dosage file.
0 markers in the range 616 are found in the geno/dosage file.
0 markers in the range 617 are found in the geno/dosage file.
0 markers in the range 618 are found in the geno/dosage file.
0 markers in the range 619 are found in the geno/dosage file.
0 markers in the range 620 are found in the geno/dosage file.
0 markers in the range 621 are found in the geno/dosage file.
0 markers in the range 622 are found in the geno/dosage file.
0 markers in the range 623 are found in the geno/dosage file.
0 markers in the range 624 are found in the geno/dosage file.
0 markers in the range 625 are found in the geno/dosage file.
0 markers in the range 626 are found in the geno/dosage file.
0 markers in the range 627 are found in the geno/dosage file.
0 markers in the range 628 are found in the geno/dosage file.
0 markers in the range 629 are found in the geno/dosage file.
0 markers in the range 630 are found in the geno/dosage file.
0 markers in the range 631 are found in the geno/dosage file.
0 markers in the range 632 are found in the geno/dosage file.
0 markers in the range 633 are found in the geno/dosage file.
0 markers in the range 634 are found in the geno/dosage file.
0 markers in the range 635 are found in the geno/dosage file.
0 markers in the range 636 are found in the geno/dosage file.
0 markers in the range 637 are found in the geno/dosage file.
0 markers in the range 638 are found in the geno/dosage file.
0 markers in the range 639 are found in the geno/dosage file.
0 markers in the range 640 are found in the geno/dosage file.
0 markers in the range 641 are found in the geno/dosage file.
0 markers in the range 642 are found in the geno/dosage file.
0 markers in the range 643 are found in the geno/dosage file.
0 markers in the range 644 are found in the geno/dosage file.
0 markers in the range 645 are found in the geno/dosage file.
0 markers in the range 646 are found in the geno/dosage file.
0 markers in the range 647 are found in the geno/dosage file.
0 markers in the range 648 are found in the geno/dosage file.
0 markers in the range 649 are found in the geno/dosage file.
0 markers in the range 650 are found in the geno/dosage file.
0 markers in the range 651 are found in the geno/dosage file.
0 markers in the range 652 are found in the geno/dosage file.
0 markers in the range 653 are found in the geno/dosage file.
0 markers in the range 654 are found in the geno/dosage file.
0 markers in the range 655 are found in the geno/dosage file.
0 markers in the range 656 are found in the geno/dosage file.
0 markers in the range 657 are found in the geno/dosage file.
0 markers in the range 658 are found in the geno/dosage file.
0 markers in the range 659 are found in the geno/dosage file.
0 markers in the range 660 are found in the geno/dosage file.
0 markers in the range 661 are found in the geno/dosage file.
0 markers in the range 662 are found in the geno/dosage file.
0 markers in the range 663 are found in the geno/dosage file.
0 markers in the range 664 are found in the geno/dosage file.
0 markers in the range 665 are found in the geno/dosage file.
0 markers in the range 666 are found in the geno/dosage file.
0 markers in the range 667 are found in the geno/dosage file.
0 markers in the range 668 are found in the geno/dosage file.
0 markers in the range 669 are found in the geno/dosage file.
0 markers in the range 670 are found in the geno/dosage file.
0 markers in the range 671 are found in the geno/dosage file.
0 markers in the range 672 are found in the geno/dosage file.
0 markers in the range 673 are found in the geno/dosage file.
0 markers in the range 674 are found in the geno/dosage file.
0 markers in the range 675 are found in the geno/dosage file.
0 markers in the range 676 are found in the geno/dosage file.
0 markers in the range 677 are found in the geno/dosage file.
0 markers in the range 678 are found in the geno/dosage file.
0 markers in the range 679 are found in the geno/dosage file.
0 markers in the range 680 are found in the geno/dosage file.
0 markers in the range 681 are found in the geno/dosage file.
0 markers in the range 682 are found in the geno/dosage file.
0 markers in the range 683 are found in the geno/dosage file.
0 markers in the range 684 are found in the geno/dosage file.
0 markers in the range 685 are found in the geno/dosage file.
0 markers in the range 686 are found in the geno/dosage file.
0 markers in the range 687 are found in the geno/dosage file.
0 markers in the range 688 are found in the geno/dosage file.
0 markers in the range 689 are found in the geno/dosage file.
0 markers in the range 690 are found in the geno/dosage file.
0 markers in the range 691 are found in the geno/dosage file.
0 markers in the range 692 are found in the geno/dosage file.
0 markers in the range 693 are found in the geno/dosage file.
0 markers in the range 694 are found in the geno/dosage file.
0 markers in the range 695 are found in the geno/dosage file.
0 markers in the range 696 are found in the geno/dosage file.
0 markers in the range 697 are found in the geno/dosage file.
0 markers in the range 698 are found in the geno/dosage file.
0 markers in the range 699 are found in the geno/dosage file.
0 markers in the range 700 are found in the geno/dosage file.
0 markers in the range 701 are found in the geno/dosage file.
0 markers in the range 702 are found in the geno/dosage file.
0 markers in the range 703 are found in the geno/dosage file.
0 markers in the range 704 are found in the geno/dosage file.
0 markers in the range 705 are found in the geno/dosage file.
0 markers in the range 706 are found in the geno/dosage file.
0 markers in the range 707 are found in the geno/dosage file.
0 markers in the range 708 are found in the geno/dosage file.
0 markers in the range 709 are found in the geno/dosage file.
0 markers in the range 710 are found in the geno/dosage file.
0 markers in the range 711 are found in the geno/dosage file.
0 markers in the range 712 are found in the geno/dosage file.
0 markers in the range 713 are found in the geno/dosage file.
0 markers in the range 714 are found in the geno/dosage file.
0 markers in the range 715 are found in the geno/dosage file.
0 markers in the range 716 are found in the geno/dosage file.
0 markers in the range 717 are found in the geno/dosage file.
0 markers in the range 718 are found in the geno/dosage file.
0 markers in the range 719 are found in the geno/dosage file.
0 markers in the range 720 are found in the geno/dosage file.
0 markers in the range 721 are found in the geno/dosage file.
0 markers in the range 722 are found in the geno/dosage file.
0 markers in the range 723 are found in the geno/dosage file.
0 markers in the range 724 are found in the geno/dosage file.
0 markers in the range 725 are found in the geno/dosage file.
0 markers in the range 726 are found in the geno/dosage file.
0 markers in the range 727 are found in the geno/dosage file.
0 markers in the range 728 are found in the geno/dosage file.
0 markers in the range 729 are found in the geno/dosage file.
0 markers in the range 730 are found in the geno/dosage file.
0 markers in the range 731 are found in the geno/dosage file.
0 markers in the range 732 are found in the geno/dosage file.
0 markers in the range 733 are found in the geno/dosage file.
0 markers in the range 734 are found in the geno/dosage file.
0 markers in the range 735 are found in the geno/dosage file.
0 markers in the range 736 are found in the geno/dosage file.
0 markers in the range 737 are found in the geno/dosage file.
0 markers in the range 738 are found in the geno/dosage file.
0 markers in the range 739 are found in the geno/dosage file.
0 markers in the range 740 are found in the geno/dosage file.
0 markers in the range 741 are found in the geno/dosage file.
0 markers in the range 742 are found in the geno/dosage file.
0 markers in the range 743 are found in the geno/dosage file.
0 markers in the range 744 are found in the geno/dosage file.
0 markers in the range 745 are found in the geno/dosage file.
0 markers in the range 746 are found in the geno/dosage file.
0 markers in the range 747 are found in the geno/dosage file.
0 markers in the range 748 are found in the geno/dosage file.
0 markers in the range 749 are found in the geno/dosage file.
0 markers in the range 750 are found in the geno/dosage file.
0 markers in the range 751 are found in the geno/dosage file.
0 markers in the range 752 are found in the geno/dosage file.
0 markers in the range 753 are found in the geno/dosage file.
0 markers in the range 754 are found in the geno/dosage file.
0 markers in the range 755 are found in the geno/dosage file.
0 markers in the range 756 are found in the geno/dosage file.
0 markers in the range 757 are found in the geno/dosage file.
0 markers in the range 758 are found in the geno/dosage file.
0 markers in the range 759 are found in the geno/dosage file.
0 markers in the range 760 are found in the geno/dosage file.
0 markers in the range 761 are found in the geno/dosage file.
0 markers in the range 762 are found in the geno/dosage file.
0 markers in the range 763 are found in the geno/dosage file.
0 markers in the range 764 are found in the geno/dosage file.
0 markers in the range 765 are found in the geno/dosage file.
0 markers in the range 766 are found in the geno/dosage file.
0 markers in the range 767 are found in the geno/dosage file.
0 markers in the range 768 are found in the geno/dosage file.
0 markers in the range 769 are found in the geno/dosage file.
0 markers in the range 770 are found in the geno/dosage file.
0 markers in the range 771 are found in the geno/dosage file.
0 markers in the range 772 are found in the geno/dosage file.
0 markers in the range 773 are found in the geno/dosage file.
0 markers in the range 774 are found in the geno/dosage file.
0 markers in the range 775 are found in the geno/dosage file.
0 markers in the range 776 are found in the geno/dosage file.
0 markers in the range 777 are found in the geno/dosage file.
0 markers in the range 778 are found in the geno/dosage file.
0 markers in the range 779 are found in the geno/dosage file.
0 markers in the range 780 are found in the geno/dosage file.
0 markers in the range 781 are found in the geno/dosage file.
0 markers in the range 782 are found in the geno/dosage file.
0 markers in the range 783 are found in the geno/dosage file.
0 markers in the range 784 are found in the geno/dosage file.
0 markers in the range 785 are found in the geno/dosage file.
0 markers in the range 786 are found in the geno/dosage file.
0 markers in the range 787 are found in the geno/dosage file.
0 markers in the range 788 are found in the geno/dosage file.
0 markers in the range 789 are found in the geno/dosage file.
0 markers in the range 790 are found in the geno/dosage file.
0 markers in the range 791 are found in the geno/dosage file.
0 markers in the range 792 are found in the geno/dosage file.
0 markers in the range 793 are found in the geno/dosage file.
0 markers in the range 794 are found in the geno/dosage file.
0 markers in the range 795 are found in the geno/dosage file.
0 markers in the range 796 are found in the geno/dosage file.
0 markers in the range 797 are found in the geno/dosage file.
0 markers in the range 798 are found in the geno/dosage file.
0 markers in the range 799 are found in the geno/dosage file.
0 markers in the range 800 are found in the geno/dosage file.
0 markers in the range 801 are found in the geno/dosage file.
0 markers in the range 802 are found in the geno/dosage file.
0 markers in the range 803 are found in the geno/dosage file.
0 markers in the range 804 are found in the geno/dosage file.
0 markers in the range 805 are found in the geno/dosage file.
0 markers in the range 806 are found in the geno/dosage file.
0 markers in the range 807 are found in the geno/dosage file.
0 markers in the range 808 are found in the geno/dosage file.
0 markers in the range 809 are found in the geno/dosage file.
0 markers in the range 810 are found in the geno/dosage file.
0 markers in the range 811 are found in the geno/dosage file.
0 markers in the range 812 are found in the geno/dosage file.
0 markers in the range 813 are found in the geno/dosage file.
0 markers in the range 814 are found in the geno/dosage file.
0 markers in the range 815 are found in the geno/dosage file.
0 markers in the range 816 are found in the geno/dosage file.
0 markers in the range 817 are found in the geno/dosage file.
0 markers in the range 818 are found in the geno/dosage file.
0 markers in the range 819 are found in the geno/dosage file.
0 markers in the range 820 are found in the geno/dosage file.
0 markers in the range 821 are found in the geno/dosage file.
0 markers in the range 822 are found in the geno/dosage file.
0 markers in the range 823 are found in the geno/dosage file.
0 markers in the range 824 are found in the geno/dosage file.
0 markers in the range 825 are found in the geno/dosage file.
0 markers in the range 826 are found in the geno/dosage file.
0 markers in the range 827 are found in the geno/dosage file.
0 markers in the range 828 are found in the geno/dosage file.
0 markers in the range 829 are found in the geno/dosage file.
0 markers in the range 830 are found in the geno/dosage file.
0 markers in the range 831 are found in the geno/dosage file.
0 markers in the range 832 are found in the geno/dosage file.
0 markers in the range 833 are found in the geno/dosage file.
0 markers in the range 834 are found in the geno/dosage file.
0 markers in the range 835 are found in the geno/dosage file.
0 markers in the range 836 are found in the geno/dosage file.
0 markers in the range 837 are found in the geno/dosage file.
0 markers in the range 838 are found in the geno/dosage file.
0 markers in the range 839 are found in the geno/dosage file.
0 markers in the range 840 are found in the geno/dosage file.
0 markers in the range 841 are found in the geno/dosage file.
0 markers in the range 842 are found in the geno/dosage file.
0 markers in the range 843 are found in the geno/dosage file.
0 markers in the range 844 are found in the geno/dosage file.
0 markers in the range 845 are found in the geno/dosage file.
0 markers in the range 846 are found in the geno/dosage file.
0 markers in the range 847 are found in the geno/dosage file.
0 markers in the range 848 are found in the geno/dosage file.
0 markers in the range 849 are found in the geno/dosage file.
0 markers in the range 850 are found in the geno/dosage file.
0 markers in the range 851 are found in the geno/dosage file.
0 markers in the range 852 are found in the geno/dosage file.
0 markers in the range 853 are found in the geno/dosage file.
0 markers in the range 854 are found in the geno/dosage file.
0 markers in the range 855 are found in the geno/dosage file.
0 markers in the range 856 are found in the geno/dosage file.
0 markers in the range 857 are found in the geno/dosage file.
0 markers in the range 858 are found in the geno/dosage file.
0 markers in the range 859 are found in the geno/dosage file.
0 markers in the range 860 are found in the geno/dosage file.
0 markers in the range 861 are found in the geno/dosage file.
0 markers in the range 862 are found in the geno/dosage file.
0 markers in the range 863 are found in the geno/dosage file.
0 markers in the range 864 are found in the geno/dosage file.
0 markers in the range 865 are found in the geno/dosage file.
0 markers in the range 866 are found in the geno/dosage file.
0 markers in the range 867 are found in the geno/dosage file.
0 markers in the range 868 are found in the geno/dosage file.
0 markers in the range 869 are found in the geno/dosage file.
0 markers in the range 870 are found in the geno/dosage file.
0 markers in the range 871 are found in the geno/dosage file.
[1] 100 100
isSparseGRM 2 TRUE
pval_cutoff_for_gxe 0.001
traitType count
Number of phenotypes to test: 1
Number of all markers to test: 4277
Number of markers in each chunk: 10000
Number of chunks for all markers: 1
(2026-01-09 00:40:05.529191) ---- Analyzing Chunk 1/1: chrom InitialChunk ----
2433 markers were tested.
write to output
user system elapsed
13.859 2.164 15.881
[1] "Analysis done! The results have been saved to 'saigeqtl_complete_results.txt'."
[2026-01-09 01:40:05,772] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: RhpcBLASctl
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: furrr
Loading required package: future
| CHR | POS | MarkerID | Allele1 | Allele2 | AC_Allele2 | AF_Allele2 | MissingRate | BETA | SE | Tstat | var | p.value | p.value.NA | Is.SPA | N | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 22 | 16569715 | 22_16569715_G_A | A | G | 106 | 0.530 | 0 | 9.658680e-16 | 54135.1 | 3.295800e-25 | 3.412270e-10 | 1 | 1 | False | 100 |
| 1 | 22 | 16569887 | 22_16569887_T_A | A | T | 133 | 0.665 | 0 | 7.073560e-16 | 61436.3 | 1.874080e-25 | 2.649420e-10 | 1 | 1 | False | 100 |
| 2 | 22 | 16570090 | 22_16570090_ACATT_A | A | ACATT | 151 | 0.755 | 0 | 5.051070e-16 | 69893.4 | 1.033980e-25 | 2.047040e-10 | 1 | 1 | False | 100 |
| 3 | 22 | 16570885 | 22_16570885_T_G | G | T | 141 | 0.705 | 0 | 1.208410e-15 | 63757.8 | 2.972680e-25 | 2.459990e-10 | 1 | 1 | False | 100 |
| 4 | 22 | 16571233 | 22_16571233_G_A | A | G | 101 | 0.505 | 0 | 5.824050e-16 | 56733.4 | 1.809460e-25 | 3.106870e-10 | 1 | 1 | False | 100 |
2. Step-by-Step Analysis#
Run each step independently for more control:
Step 1 Only: Fit Null Model#
step1_results = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="gene1_step1",
steps=[1], # Only Step 1
sample_covariates=["gPCs"],
tol=0.00001,
maxiter=20,
use_grm_to_fit_null=False,
overwrite_variance_ratio_file=True,
run=True,
)
print(step1_results)
Writing FAM... done.
Writing BIM... done.
[2026-01-09 01:40:06,768] INFO:cellink.tl.external._saigeqtl: Running Step 1: Fitting null model
[2026-01-09 01:40:06,769] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step1_fitNULLGLMM_qtl.R --phenoFile=gene1_step1_phenotype.txt --phenoCol=ENSG00000273362 --sampleIDColinphenoFile=IND_ID --traitType=count --plinkFile=gene1_step1 --outputPrefix=gene1_step1 --tol=1e-05 --LOCO=FALSE --useGRMtoFitNULL=FALSE --IsOverwriteVarianceRatioFile=TRUE --covarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19 --sampleCovarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19
[2026-01-09 01:40:24,143] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] optparse_1.7.5 SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] data.table_1.17.6 RcppParallel_5.1.9 lattice_0.22-7
$plinkFile
[1] "gene1_step1"
$bedFile
[1] ""
$bimFile
[1] ""
$famFile
[1] ""
$phenoFile
[1] "gene1_step1_phenotype.txt"
$phenoCol
[1] "ENSG00000273362"
$isRemoveZerosinPheno
[1] FALSE
$traitType
[1] "count"
$invNormalize
[1] FALSE
$covarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19"
$sampleCovarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19"
$longlCol
[1] ""
$qCovarColList
[1] ""
$sampleIDColinphenoFile
[1] "IND_ID"
$cellIDColinphenoFile
[1] ""
$tol
[1] 1e-05
$maxiter
[1] 20
$tolPCG
[1] 1e-05
$maxiterPCG
[1] 500
$nThreads
[1] 1
$SPAcutoff
[1] 2
$numRandomMarkerforVarianceRatio
[1] 30
$skipModelFitting
[1] FALSE
$skipVarianceRatioEstimation
[1] FALSE
$memoryChunk
[1] 2
$tauInit
[1] "0,0"
$LOCO
[1] FALSE
$isLowMemLOCO
[1] FALSE
$traceCVcutoff
[1] 0.0025
$nrun
[1] 30
$ratioCVcutoff
[1] 0.001
$outputPrefix
[1] "gene1_step1"
$outputPrefix_varRatio
[1] ""
$IsOverwriteVarianceRatioFile
[1] TRUE
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$isCateVarianceRatio
[1] FALSE
$relatednessCutoff
[1] 0
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$isCovariateTransform
[1] TRUE
$isDiagofKinSetAsOne
[1] FALSE
$useSparseGRMtoFitNULL
[1] FALSE
$useSparseGRMforVarRatio
[1] FALSE
$minMAFforGRM
[1] 0.01
$maxMissingRateforGRM
[1] 0.15
$minCovariateCount
[1] -1
$includeNonautoMarkersforVarRatio
[1] FALSE
$FemaleOnly
[1] FALSE
$MaleOnly
[1] FALSE
$sexCol
[1] ""
$FemaleCode
[1] "1"
$MaleCode
[1] "0"
$isCovariateOffset
[1] TRUE
$SampleIDIncludeFile
[1] ""
$VmatFilelist
[1] ""
$VmatSampleFilelist
[1] ""
$useGRMtoFitNULL
[1] FALSE
$isStoreSigma
[1] TRUE
$isShrinkModelOutput
[1] TRUE
$isExportResiduals
[1] FALSE
$help
[1] FALSE
tauInit is 0 0
cateVarRatioMinMACVecExclude is 10 20.5
cateVarRatioMaxMACVecInclude is 20.5
No GRM will be used to fit the NULL model and nThreads is set to 1
The variance ratio file gene1_step1.varianceRatio.txt already exists. IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten
100 samples have genotypes
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
[1] "HERERE2"
formula is ENSG00000273362~sex+age+gPCs_0+gPCs_1+gPCs_2+gPCs_3+gPCs_4+gPCs_5+gPCs_6+gPCs_7+gPCs_8+gPCs_9+gPCs_10+gPCs_11+gPCs_12+gPCs_13+gPCs_14+gPCs_15+gPCs_16+gPCs_17+gPCs_18+gPCs_19
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
4756 samples have non-missing phenotypes
Duplicated sample IDs are detected in the phenotype file. Assuming repeated measurements
[1] "Test"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
4756 observations will be used for analysis
[1] "Test3"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "Test4"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
qr transformation has been performed on covariates
colnames(data.new) is ENSG00000273362 minus1 sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19
out.transform$Param.transform$qrr: 23 23
[1] "isCovariateOffset=TRUE, so fixed effects coefficnets won't be estimated."
[1] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806"
[6] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_518"
[11] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[16] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[21] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[26] "OneK1K_518" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[31] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[36] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[41] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[46] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[51] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[56] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[61] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[66] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[71] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[76] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[81] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[86] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[91] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_588"
[96] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[101] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[106] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[111] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[116] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[121] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[126] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_1061" "OneK1K_1061"
[131] "OneK1K_1061" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[136] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[141] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[146] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[151] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[156] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[161] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[166] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[171] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[176] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[181] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[186] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[191] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[196] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[1] TRUE
numofV 0
[1] "HERE"
[1] "HERE1"
[1] FALSE
num_Kmat 2
ptr_gNULLGENOobj->g_minMACVarRatio 20
ptr_gNULLGENOobj->g_maxMACVarRatio -1
Markers in the Plink file with MAF < 0.01 will be removed before constructing GRM
Markers in the Plink file with missing rate > 0.15 will be removed before constructing GRM
ENSG00000273362 is a count trait
glm:
Call: glm(formula = formula.new, family = "poisson", data = data.new,
weights = varWeights, offset = covoffset)
Coefficients:
(Intercept)
-27.3
Degrees of Freedom: 4755 Total (i.e. Null); 4755 Residual
Null Deviance: 2.42e-10
Residual Deviance: 1.321e-08 AIC: 2
[1] "isStoreSigma"
[1] TRUE
Start fitting the NULL GLMM
user system elapsed
14.328 2.034 16.278
user system elapsed
14.384 2.034 16.335
[1] "Start reading genotype plink file here"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "length(indicatorGenoSamplesWithPheno)"
[1] 4756
[1] "Genotype reading is done"
tauInit[1] 0 0
fixtau 1 0
tauInit 1 0
inital tau is 1 0.1
[1] "tau"
[1] 1.0 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
(Intercept)
-27.30259
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
[1] "tau0_q2 a"
[1] 0.1
[1] "idxtau"
[1] 2
[1] "re$YPAPY"
[,1]
[1,] 1.039092e-18
[1] "re$Trace"
[,1]
[1,] 2.303134e-09
Variance component estimates:
[1] 1.0 0.1
Iteration 1 1 0.1 :
tau0_v1: 1 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
t_end_Get_Coef - t_begin_Get_Coef
user system elapsed
0.001 0.000 0.001
check 1
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
check 2
score1
-2.3031e-09
YPAPY
1.0391e-18
Trace
2.3031e-09
score
-2.3031e-09
i 0
i 1
t_end_fitglmmaiRPCG - t_begin_fitglmmaiRPCG
user system elapsed
0.029 0.001 0.030
[1] 0.000000e+00 7.450232e-09
tau: 1 0.1
tau0: 1 0.1
Final 1 0.1 :
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
4.1159e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -29.30295
[1] "alpha"
[,1]
[1,] -29.30295
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -29.30295
t_end_null - t_begin, fitting the NULL model without LOCO took
user system elapsed
0.093 0.001 0.094
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
isStoreSigma is TRUE
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
user system elapsed
14.485 2.037 16.438
t_end - t_begin, fitting the NULL model took
user system elapsed
0.157 0.003 0.160
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[25] 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[49] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[73] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4
[97] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
[121] 4 4 4 4 4 4 4 4 5 5 5 6 6 6 6 6 6 6 6 6 6 6 6 6
[145] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[169] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[193] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[217] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[241] 6 6 6 6 6 6 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[265] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[289] 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 9 9
[313] 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 10
[337] 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11
[361] 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 13 13 13 13
[385] 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
[409] 13 13 14 14 14 14 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16
[433] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17
[457] 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18
[481] 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 19 19 19 19 19 19
[505] 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19
[529] 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[553] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[577] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[601] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[625] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[649] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[673] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[697] 20 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22
[721] 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22
[745] 22 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
[769] 23 23 23 23 23 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24
[793] 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 25 25 25 25 25
[817] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[841] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[865] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[889] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[913] 26 26 26 26 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[937] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[961] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[985] 27 27 27 27 27 27 27 27 28 28 28 28 28 28 28 28
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 ENSG00000273362
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 0
IndexPheno IndexGeno
3403 1 1
3404 2 1
3405 3 1
3406 4 1
3407 5 1
3408 6 1
[1] "HEREHRE"
nbyte: 25
nbyte: 25
reserve: 115479
M: 4277, N: 100
setgeno mark1
setgeno mark2
3516 markers with MAF >= 0.01 and missing rate <= 0.15
time: 9.749
Start estimating variance ratios
Family: poisson
Link function: log
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
length(MACvector): 3516
length(MACvector_forVarRatio): 521
Only one variance ratio will be estimated using randomly selected markers with MAC >= 20
29 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
257 22 22_16708242_C_T 0 16708242 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2505
iter from getPCG1ofSigmaAndVector 1
AC 2354
S is -2.447558e-24
var1 is 1.911061e-10
p_exact 1
var2sparseGRM Here 1.911062e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2354
var1 1.911061e-10
var2null 1.911061e-10
var2null_noXadj 2.620976e-10
98 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
732 22 22_16849519_G_T 0 16849519 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1548
iter from getPCG1ofSigmaAndVector 1
AC 3852
S is -1.19253e-24
var1 is 2.561159e-10
p_exact 1
var2sparseGRM Here 2.561161e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3852
var1 2.561159e-10
var2null 2.561159e-10
var2null_noXadj 3.799173e-10
45 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
365 22 22_16743395_C_A 0 16743395 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1778
S is -5.863572e-25
var1 is 2.020268e-10
p_exact 1
var2sparseGRM Here 2.02027e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1778
var1 2.020268e-10
var2null 2.020268e-10
var2null_noXadj 2.794007e-10
156 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1141 22 22_16962373_T_A 0 16962373 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
377 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 0 0 2 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2888 22 22_17318326_C_T 0 17318326 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3016
iter from getPCG1ofSigmaAndVector 1
AC 1958
S is 1.091594e-24
var1 is 1.748766e-10
p_exact 1
var2sparseGRM Here 1.748766e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1958
var1 1.748766e-10
var2null 1.748766e-10
var2null_noXadj 3.004277e-10
202 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1670 22 22_17087008_A_G 0 17087008 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
228 th marker in geno 1
MAC: 97
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 0 1 1 2 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1820 22 22_17125423_C_CA 0 17125423 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1434
iter from getPCG1ofSigmaAndVector 1
AC 4638
S is 3.054671e-24
var1 is 3.272003e-10
p_exact 1
var2sparseGRM Here 3.272005e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4638
var1 3.272003e-10
var2null 3.272003e-10
var2null_noXadj 5.172127e-10
212 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 1 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1729 22 22_17106625_T_C 0 17106625 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3123
iter from getPCG1ofSigmaAndVector 1
AC 1761
S is 7.608911e-25
var1 is 1.584355e-10
p_exact 1
var2sparseGRM Here 1.584355e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1761
var1 1.584355e-10
var2null 1.584355e-10
var2null_noXadj 2.572716e-10
492 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4005 22 22_17525225_C_T 0 17525225 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
477 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3916 22 22_17511574_A_G 0 17511574 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3747
iter from getPCG1ofSigmaAndVector 1
AC 1077
S is -3.20694e-25
var1 is 1.279881e-10
p_exact 1
var2sparseGRM Here 1.279882e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1077
var1 1.279881e-10
var2null 1.279882e-10
var2null_noXadj 1.820916e-10
209 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 2 2 2 2 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1717 22 22_17104551_C_T 0 17104551 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1403
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is -2.857582e-24
var1 is 2.749479e-10
p_exact 1
var2sparseGRM Here 2.749481e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 2.749479e-10
var2null 2.749479e-10
var2null_noXadj 4.93364e-10
291 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2303 22 22_17195422_G_A 0 17195422 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3534
iter from getPCG1ofSigmaAndVector 1
AC 1575
S is 7.4808e-25
var1 is 1.891389e-10
p_exact 1
var2sparseGRM Here 1.891391e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1575
var1 1.891389e-10
var2null 1.89139e-10
var2null_noXadj 3.397109e-10
81 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
614 22 22_16822493_C_T 0 16822493 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1281
iter from getPCG1ofSigmaAndVector 1
AC 4492
S is 2.095215e-24
var1 is 2.637957e-10
p_exact 1
var2sparseGRM Here 2.637958e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4492
var1 2.637957e-10
var2null 2.637957e-10
var2null_noXadj 4.479227e-10
79 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
605 22 22_16821873_G_C 0 16821873 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1830
iter from getPCG1ofSigmaAndVector 1
AC 3568
S is -5.426227e-25
var1 is 2.250768e-10
p_exact 1
var2sparseGRM Here 2.250769e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3568
var1 2.250768e-10
var2null 2.250768e-10
var2null_noXadj 4.34582e-10
509 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 2 0 0 2 2 0 1 2 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 0
CHR 22
V1 V2 V3 V4 V5 V6
4190 22 22_17564857_C_CAAAAAAAAAAA 0 17564857 C CAAAAAAAAAAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1354
iter from getPCG1ofSigmaAndVector 1
AC 4575
S is 3.475128e-24
var1 is 2.746995e-10
p_exact 1
var2sparseGRM Here 2.746996e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4575
var1 2.746995e-10
var2null 2.746995e-10
var2null_noXadj 4.758986e-10
496 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 0 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4033 22 22_17531010_A_G 0 17531010 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3289
iter from getPCG1ofSigmaAndVector 1
AC 1622
S is 6.507787e-25
var1 is 1.798199e-10
p_exact 1
var2sparseGRM Here 1.7982e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1622
var1 1.798199e-10
var2null 1.798199e-10
var2null_noXadj 2.604154e-10
362 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2803 22 22_17302684_T_C 0 17302684 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1501
iter from getPCG1ofSigmaAndVector 1
AC 4307
S is 7.681612e-25
var1 is 2.50358e-10
p_exact 1
var2sparseGRM Here 2.503581e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4307
var1 2.50358e-10
var2null 2.50358e-10
var2null_noXadj 4.72288e-10
64 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
518 22 22_16801041_G_A 0 16801041 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3889
S is 4.154646e-25
var1 is 2.153042e-10
p_exact 1
var2sparseGRM Here 2.153043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3889
var1 2.153042e-10
var2null 2.153042e-10
var2null_noXadj 4.40872e-10
440 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3510 22 22_17441874_G_C 0 17441874 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
511 th marker in geno 1
MAC: 74
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4205 22 22_17567322_A_G 0 17567322 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2171
iter from getPCG1ofSigmaAndVector 1
AC 3183
S is 2.085471e-24
var1 is 2.680107e-10
p_exact 1
var2sparseGRM Here 2.680108e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3183
var1 2.680107e-10
var2null 2.680107e-10
var2null_noXadj 4.2986e-10
489 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3985 22 22_17523014_A_AGGGG 0 17523014 A AGGGG
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2724
iter from getPCG1ofSigmaAndVector 1
AC 2268
S is -2.175552e-24
var1 is 1.469711e-10
p_exact 1
var2sparseGRM Here 1.469711e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2268
var1 1.469711e-10
var2null 1.469711e-10
var2null_noXadj 3.283367e-10
216 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1738 22 22_17108677_C_T 0 17108677 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2975
iter from getPCG1ofSigmaAndVector 1
AC 2053
S is -4.137071e-25
var1 is 2.373018e-10
p_exact 1
var2sparseGRM Here 2.373018e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2053
var1 2.373018e-10
var2null 2.373018e-10
var2null_noXadj 3.438314e-10
78 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
600 22 22_16821568_C_G 0 16821568 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3305
iter from getPCG1ofSigmaAndVector 1
AC 1503
S is 8.573971e-26
var1 is 1.270707e-10
p_exact 1
var2sparseGRM Here 1.270707e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1503
var1 1.270707e-10
var2null 1.270707e-10
var2null_noXadj 2.128624e-10
444 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3537 22 22_17445692_G_A 0 17445692 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
227 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1819 22 22_17125117_T_TA 0 17125117 T TA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2824
iter from getPCG1ofSigmaAndVector 1
AC 2307
S is -8.466181e-25
var1 is 2.682152e-10
p_exact 1
var2sparseGRM Here 2.682154e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2307
var1 2.682152e-10
var2null 2.682152e-10
var2null_noXadj 3.641289e-10
259 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2094 22 22_17170409_AAAAAAT_A 0 17170409 AAAAAAT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1738
S is 8.149564e-25
var1 is 1.690214e-10
p_exact 1
var2sparseGRM Here 1.690214e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1738
var1 1.690214e-10
var2null 1.690214e-10
var2null_noXadj 2.678111e-10
40 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
334 22 22_16738360_T_A 0 16738360 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3614
iter from getPCG1ofSigmaAndVector 1
AC 1214
S is 6.221904e-25
var1 is 1.265151e-10
p_exact 1
var2sparseGRM Here 1.265152e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1214
var1 1.265151e-10
var2null 1.265151e-10
var2null_noXadj 1.974943e-10
15 th marker in geno 1
MAC: 58
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
164 22 22_16678727_G_A 0 16678727 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2401
iter from getPCG1ofSigmaAndVector 1
AC 2703
S is -1.590546e-24
var1 is 2.318528e-10
p_exact 1
var2sparseGRM Here 2.318529e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2703
var1 2.318528e-10
var2null 2.318528e-10
var2null_noXadj 3.508839e-10
211 th marker in geno 1
MAC: 94
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 1 1 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1725 22 22_17105724_G_C 0 17105724 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1308
iter from getPCG1ofSigmaAndVector 1
AC 4560
S is -4.742897e-24
var1 is 2.787683e-10
p_exact 1
var2sparseGRM Here 2.787684e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4560
var1 2.787683e-10
var2null 2.787683e-10
var2null_noXadj 4.662892e-10
261 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2123 22 22_17173199_C_T 0 17173199 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2696
S is 1.41061e-24
var1 is 1.886188e-10
p_exact 1
var2sparseGRM Here 1.886189e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2696
var1 1.886188e-10
var2null 1.886188e-10
var2null_noXadj 2.770454e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229
CV for variance ratio estimate using 30 markers is 0.004253911 > 0.001
try 40 markers
269 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2164 22 22_17175884_G_GT 0 17175884 G GT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2696
S is 1.41061e-24
var1 is 1.886188e-10
p_exact 1
var2sparseGRM Here 1.886189e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2696
var1 1.886188e-10
var2null 1.886188e-10
var2null_noXadj 2.770454e-10
38 th marker in geno 1
MAC: 83
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 0 1 1 1 2 0 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
306 22 22_16726908_G_T 0 16726908 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1525
iter from getPCG1ofSigmaAndVector 1
AC 4262
S is -3.97543e-24
var1 is 3.594641e-10
p_exact 1
var2sparseGRM Here 3.594645e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4262
var1 3.594641e-10
var2null 3.594641e-10
var2null_noXadj 4.744979e-10
118 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
862 22 22_16878208_T_C 0 16878208 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2847
iter from getPCG1ofSigmaAndVector 1
AC 1980
S is -7.3306e-25
var1 is 1.541723e-10
p_exact 1
var2sparseGRM Here 1.541723e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1980
var1 1.541723e-10
var2null 1.541723e-10
var2null_noXadj 2.521049e-10
19 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
181 22 22_16688797_GAA_G 0 16688797 GAA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3137
iter from getPCG1ofSigmaAndVector 1
AC 1789
S is 4.323084e-25
var1 is 1.838207e-10
p_exact 1
var2sparseGRM Here 1.838208e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1789
var1 1.838207e-10
var2null 1.838207e-10
var2null_noXadj 2.737403e-10
107 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
790 22 22_16861810_T_C 0 16861810 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3636
iter from getPCG1ofSigmaAndVector 1
AC 1202
S is -2.370843e-26
var1 is 1.168809e-10
p_exact 1
var2sparseGRM Here 1.168809e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1202
var1 1.168809e-10
var2null 1.168809e-10
var2null_noXadj 2.036159e-10
372 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 0 2 0 0 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 2
CHR 22
V1 V2 V3 V4 V5 V6
2861 22 22_17310674_T_C 0 17310674 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2208
iter from getPCG1ofSigmaAndVector 1
AC 2942
S is 3.683324e-24
var1 is 2.37273e-10
p_exact 1
var2sparseGRM Here 2.372732e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2942
var1 2.37273e-10
var2null 2.37273e-10
var2null_noXadj 3.596099e-10
514 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4215 22 22_17570571_G_T 0 17570571 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2123
iter from getPCG1ofSigmaAndVector 1
AC 3527
S is -5.723167e-24
var1 is 2.967774e-10
p_exact 1
var2sparseGRM Here 2.967775e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3527
var1 2.967774e-10
var2null 2.967774e-10
var2null_noXadj 5.084939e-10
67 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
539 22 22_16805822_T_A 0 16805822 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3889
S is 4.154646e-25
var1 is 2.153042e-10
p_exact 1
var2sparseGRM Here 2.153043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3889
var1 2.153042e-10
var2null 2.153042e-10
var2null_noXadj 4.40872e-10
130 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
949 22 22_16914834_C_G 0 16914834 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3590
iter from getPCG1ofSigmaAndVector 1
AC 1238
S is 6.451746e-25
var1 is 1.24676e-10
p_exact 1
var2sparseGRM Here 1.246761e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1238
var1 1.24676e-10
var2null 1.24676e-10
var2null_noXadj 1.994771e-10
248 th marker in geno 1
MAC: 55
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1975 22 22_17151727_TAAAAAA_T 0 17151727 TAAAAAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2655
iter from getPCG1ofSigmaAndVector 1
AC 2315
S is 2.469905e-24
var1 is 2.237693e-10
p_exact 1
var2sparseGRM Here 2.237694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2315
var1 2.237693e-10
var2null 2.237694e-10
var2null_noXadj 3.084451e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755
CV for variance ratio estimate using 40 markers is 0.003165943 > 0.001
try 50 markers
263 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2136 22 22_17174211_C_T 0 17174211 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2097
iter from getPCG1ofSigmaAndVector 1
AC 2977
S is 7.564482e-25
var1 is 2.317111e-10
p_exact 1
var2sparseGRM Here 2.317112e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2977
var1 2.317111e-10
var2null 2.317111e-10
var2null_noXadj 3.353139e-10
475 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3910 22 22_17510346_C_T 0 17510346 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3421
iter from getPCG1ofSigmaAndVector 1
AC 1382
S is 1.261635e-24
var1 is 1.396816e-10
p_exact 1
var2sparseGRM Here 1.396817e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1382
var1 1.396816e-10
var2null 1.396816e-10
var2null_noXadj 2.026389e-10
125 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
917 22 22_16906964_G_A 0 16906964 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3729
iter from getPCG1ofSigmaAndVector 1
AC 1099
S is 2.650068e-25
var1 is 1.198167e-10
p_exact 1
var2sparseGRM Here 1.198168e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1099
var1 1.198167e-10
var2null 1.198167e-10
var2null_noXadj 1.858969e-10
466 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 0 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3856 22 22_17499058_T_C 0 17499058 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2848
iter from getPCG1ofSigmaAndVector 1
AC 2355
S is 1.459885e-24
var1 is 2.27525e-10
p_exact 1
var2sparseGRM Here 2.275251e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2355
var1 2.27525e-10
var2null 2.27525e-10
var2null_noXadj 3.915373e-10
8 th marker in geno 1
MAC: 43
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 0 0 0 0 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
110 22 22_16594856_C_CT 0 16594856 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3119
iter from getPCG1ofSigmaAndVector 1
AC 1699
S is -2.203181e-24
var1 is 1.463611e-10
p_exact 1
var2sparseGRM Here 1.463612e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1699
var1 1.463611e-10
var2null 1.463611e-10
var2null_noXadj 2.332095e-10
244 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 1 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1952 22 22_17147758_C_T 0 17147758 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2625
iter from getPCG1ofSigmaAndVector 1
AC 2457
S is -7.982515e-25
var1 is 2.751918e-10
p_exact 1
var2sparseGRM Here 2.75192e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2457
var1 2.751918e-10
var2null 2.751918e-10
var2null_noXadj 3.462799e-10
223 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1787 22 22_17117420_C_T 0 17117420 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2799
iter from getPCG1ofSigmaAndVector 1
AC 2404
S is 8.6521e-25
var1 is 2.442336e-10
p_exact 1
var2sparseGRM Here 2.442337e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2404
var1 2.442336e-10
var2null 2.442336e-10
var2null_noXadj 3.977202e-10
95 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
704 22 22_16842702_G_A 0 16842702 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3816
iter from getPCG1ofSigmaAndVector 1
AC 1022
S is -4.525411e-25
var1 is 1.315691e-10
p_exact 1
var2sparseGRM Here 1.315691e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1022
var1 1.315691e-10
var2null 1.315691e-10
var2null_noXadj 2.030677e-10
198 th marker in geno 1
MAC: 96
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1627 22 22_17074025_G_A 0 17074025 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1652
iter from getPCG1ofSigmaAndVector 1
AC 4607
S is -2.003e-24
var1 is 3.557996e-10
p_exact 1
var2sparseGRM Here 3.557999e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4607
var1 3.557996e-10
var2null 3.557997e-10
var2null_noXadj 5.922073e-10
180 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1517 22 22_17046605_G_C 0 17046605 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1696
iter from getPCG1ofSigmaAndVector 1
AC 4563
S is -2.340809e-24
var1 is 3.541055e-10
p_exact 1
var2sparseGRM Here 3.541058e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4563
var1 3.541055e-10
var2null 3.541056e-10
var2null_noXadj 6.009567e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364
CV for variance ratio estimate using 50 markers is 0.002440275 > 0.001
try 60 markers
415 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3261 22 22_17408995_A_T 0 17408995 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 841
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 2.754601e-24
var1 is 2.020824e-10
p_exact 1
var2sparseGRM Here 2.020825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.020824e-10
var2null 2.020824e-10
var2null_noXadj 2.851867e-10
258 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2090 22 22_17170041_C_T 0 17170041 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1738
S is 8.149564e-25
var1 is 1.690214e-10
p_exact 1
var2sparseGRM Here 1.690214e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1738
var1 1.690214e-10
var2null 1.690214e-10
var2null_noXadj 2.678111e-10
189 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1556 22 22_17054364_T_C 0 17054364 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
31 th marker in geno 1
MAC: 61
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
269 22 22_16713436_T_C 0 16713436 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1649
iter from getPCG1ofSigmaAndVector 1
AC 3725
S is 1.456439e-24
var1 is 2.46971e-10
p_exact 1
var2sparseGRM Here 2.469712e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3725
var1 2.46971e-10
var2null 2.46971e-10
var2null_noXadj 4.049186e-10
105 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 0 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
774 22 22_16859187_A_G 0 16859187 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2565
iter from getPCG1ofSigmaAndVector 1
AC 2668
S is 1.219263e-26
var1 is 2.098046e-10
p_exact 1
var2sparseGRM Here 2.098047e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2668
var1 2.098046e-10
var2null 2.098046e-10
var2null_noXadj 4.084232e-10
284 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2265 22 22_17187678_A_G 0 17187678 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2620
iter from getPCG1ofSigmaAndVector 1
AC 2289
S is -3.581302e-24
var1 is 1.781993e-10
p_exact 1
var2sparseGRM Here 1.781994e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2289
var1 1.781993e-10
var2null 1.781993e-10
var2null_noXadj 2.897403e-10
383 th marker in geno 1
MAC: 25
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2917 22 22_17323505_T_C 0 17323505 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3926
iter from getPCG1ofSigmaAndVector 1
AC 953
S is 4.145874e-25
var1 is 1.143702e-10
p_exact 1
var2sparseGRM Here 1.143702e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 953
var1 1.143702e-10
var2null 1.143702e-10
var2null_noXadj 1.937254e-10
136 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 2 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
975 22 22_16924021_C_G 0 16924021 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1568
iter from getPCG1ofSigmaAndVector 1
AC 3811
S is -4.228698e-24
var1 is 2.946292e-10
p_exact 1
var2sparseGRM Here 2.946293e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3811
var1 2.946292e-10
var2null 2.946292e-10
var2null_noXadj 3.805914e-10
190 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1565 22 22_17055665_A_G 0 17055665 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
264 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2137 22 22_17174286_G_C 0 17174286 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1387
iter from getPCG1ofSigmaAndVector 1
AC 3709
S is 4.247151e-24
var1 is 1.671652e-10
p_exact 1
var2sparseGRM Here 1.671653e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3709
var1 1.671652e-10
var2null 1.671652e-10
var2null_noXadj 2.812566e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514
CV for variance ratio estimate using 60 markers is 0.00200029 > 0.001
try 70 markers
39 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
323 22 22_16733220_A_G 0 16733220 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3614
iter from getPCG1ofSigmaAndVector 1
AC 1214
S is 6.221904e-25
var1 is 1.265151e-10
p_exact 1
var2sparseGRM Here 1.265152e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1214
var1 1.265151e-10
var2null 1.265151e-10
var2null_noXadj 1.974943e-10
310 th marker in geno 1
MAC: 95
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 0 2 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2445 22 22_17216771_A_C 0 17216771 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1397
iter from getPCG1ofSigmaAndVector 1
AC 4055
S is -2.648907e-24
var1 is 2.07781e-10
p_exact 1
var2sparseGRM Here 2.077811e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4055
var1 2.07781e-10
var2null 2.07781e-10
var2null_noXadj 4.08645e-10
304 th marker in geno 1
MAC: 91
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 1 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2412 22 22_17211494_G_A 0 17211494 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1234
iter from getPCG1ofSigmaAndVector 1
AC 4628
S is -3.614876e-25
var1 is 2.535832e-10
p_exact 1
var2sparseGRM Here 2.535833e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4628
var1 2.535832e-10
var2null 2.535832e-10
var2null_noXadj 4.47393e-10
252 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2029 22 22_17160649_GA_G 0 17160649 GA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2982
iter from getPCG1ofSigmaAndVector 1
AC 2014
S is -1.064451e-24
var1 is 2.481048e-10
p_exact 1
var2sparseGRM Here 2.481049e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2014
var1 2.481048e-10
var2null 2.481048e-10
var2null_noXadj 3.179093e-10
397 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3059 22 22_17358468_C_T 0 17358468 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1408
iter from getPCG1ofSigmaAndVector 1
AC 4358
S is 5.205845e-24
var1 is 3.474116e-10
p_exact 1
var2sparseGRM Here 3.474119e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4358
var1 3.474116e-10
var2null 3.474116e-10
var2null_noXadj 4.480805e-10
393 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3045 22 22_17353687_T_C 0 17353687 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1392
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is 6.121056e-24
var1 is 3.073406e-10
p_exact 1
var2sparseGRM Here 3.073408e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 3.073406e-10
var2null 3.073406e-10
var2null_noXadj 4.9917e-10
428 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
3392 22 22_17427809_A_G 0 17427809 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3954
iter from getPCG1ofSigmaAndVector 1
AC 870
S is -5.028515e-26
var1 is 1.254682e-10
p_exact 1
var2sparseGRM Here 1.254682e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 870
var1 1.254682e-10
var2null 1.254682e-10
var2null_noXadj 1.620206e-10
417 th marker in geno 1
MAC: 88
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3298 22 22_17417019_CT_C 0 17417019 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1164
iter from getPCG1ofSigmaAndVector 1
AC 4331
S is 2.730797e-24
var1 is 2.440372e-10
p_exact 1
var2sparseGRM Here 2.440373e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4331
var1 2.440372e-10
var2null 2.440372e-10
var2null_noXadj 3.505081e-10
36 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
299 22 22_16724286_T_C 0 16724286 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3558
iter from getPCG1ofSigmaAndVector 1
AC 1270
S is 1.621254e-24
var1 is 1.295267e-10
p_exact 1
var2sparseGRM Here 1.295268e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1270
var1 1.295267e-10
var2null 1.295267e-10
var2null_noXadj 2.022097e-10
155 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1122 22 22_16958936_G_A 0 16958936 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
CV for variance ratio estimate using 70 markers is 0.001829244 > 0.001
try 80 markers
162 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1201 22 22_16975883_A_C 0 16975883 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4274
S is -2.983535e-24
var1 is 2.638024e-10
p_exact 1
var2sparseGRM Here 2.638025e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4274
var1 2.638024e-10
var2null 2.638024e-10
var2null_noXadj 5.527296e-10
293 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2318 22 22_17196323_C_CA 0 17196323 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2536
iter from getPCG1ofSigmaAndVector 1
AC 2703
S is 2.721993e-24
var1 is 2.683981e-10
p_exact 1
var2sparseGRM Here 2.683983e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2703
var1 2.683981e-10
var2null 2.683981e-10
var2null_noXadj 4.028041e-10
27 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
246 22 22_16705760_TA_T 0 16705760 TA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1691
iter from getPCG1ofSigmaAndVector 1
AC 3683
S is 1.564128e-24
var1 is 2.576679e-10
p_exact 1
var2sparseGRM Here 2.57668e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3683
var1 2.576679e-10
var2null 2.576679e-10
var2null_noXadj 4.096401e-10
58 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
477 22 22_16788186_C_T 0 16788186 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2719
iter from getPCG1ofSigmaAndVector 1
AC 2037
S is -2.836113e-24
var1 is 1.381818e-10
p_exact 1
var2sparseGRM Here 1.381819e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2037
var1 1.381818e-10
var2null 1.381819e-10
var2null_noXadj 2.274347e-10
48 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 1 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
384 22 22_16747765_CT_C 0 16747765 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2030
iter from getPCG1ofSigmaAndVector 1
AC 3386
S is -4.638452e-24
var1 is 2.792877e-10
p_exact 1
var2sparseGRM Here 2.792879e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3386
var1 2.792877e-10
var2null 2.792878e-10
var2null_noXadj 4.518904e-10
127 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
930 22 22_16908129_T_A 0 16908129 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3729
iter from getPCG1ofSigmaAndVector 1
AC 1099
S is 2.650068e-25
var1 is 1.198167e-10
p_exact 1
var2sparseGRM Here 1.198168e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1099
var1 1.198167e-10
var2null 1.198167e-10
var2null_noXadj 1.858969e-10
367 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2842 22 22_17307364_G_A 0 17307364 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2066
iter from getPCG1ofSigmaAndVector 1
AC 3397
S is 1.83874e-24
var1 is 2.369872e-10
p_exact 1
var2sparseGRM Here 2.369873e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3397
var1 2.369872e-10
var2null 2.369872e-10
var2null_noXadj 4.480572e-10
123 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
886 22 22_16886615_AT_A 0 16886615 AT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3843
iter from getPCG1ofSigmaAndVector 1
AC 1057
S is 4.325735e-25
var1 is 1.35786e-10
p_exact 1
var2sparseGRM Here 1.35786e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1057
var1 1.35786e-10
var2null 1.35786e-10
var2null_noXadj 2.085715e-10
94 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
686 22 22_16839591_T_C 0 16839591 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3894
iter from getPCG1ofSigmaAndVector 1
AC 944
S is -6.908465e-25
var1 is 1.240043e-10
p_exact 1
var2sparseGRM Here 1.240043e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 944
var1 1.240043e-10
var2null 1.240043e-10
var2null_noXadj 1.861653e-10
279 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2242 22 22_17184523_T_C 0 17184523 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3571
iter from getPCG1ofSigmaAndVector 1
AC 1297
S is -2.184577e-25
var1 is 9.989261e-11
p_exact 1
var2sparseGRM Here 9.989264e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1297
var1 9.989261e-11
var2null 9.989262e-11
var2null_noXadj 2.193226e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597
CV for variance ratio estimate using 80 markers is 0.001610003 > 0.001
try 90 markers
236 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 1 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1864 22 22_17131854_G_A 0 17131854 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2639
iter from getPCG1ofSigmaAndVector 1
AC 2712
S is -3.435647e-26
var1 is 2.77587e-10
p_exact 1
var2sparseGRM Here 2.775872e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2712
var1 2.77587e-10
var2null 2.77587e-10
var2null_noXadj 4.515445e-10
450 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3566 22 22_17448910_C_T 0 17448910 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
166 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1369 22 22_17014255_C_T 0 17014255 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3405
iter from getPCG1ofSigmaAndVector 1
AC 1467
S is 2.641359e-25
var1 is 1.654633e-10
p_exact 1
var2sparseGRM Here 1.654634e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1467
var1 1.654633e-10
var2null 1.654633e-10
var2null_noXadj 2.343161e-10
413 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3251 22 22_17406562_G_A 0 17406562 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 841
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 2.754601e-24
var1 is 2.020824e-10
p_exact 1
var2sparseGRM Here 2.020825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.020824e-10
var2null 2.020824e-10
var2null_noXadj 2.851867e-10
68 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
543 22 22_16806309_C_CAT 0 16806309 C CAT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3625
iter from getPCG1ofSigmaAndVector 1
AC 1143
S is 2.171955e-25
var1 is 1.083828e-10
p_exact 1
var2sparseGRM Here 1.083828e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1143
var1 1.083828e-10
var2null 1.083828e-10
var2null_noXadj 1.679953e-10
276 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 1 1 1 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2207 22 22_17179611_C_G 0 17179611 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1048
iter from getPCG1ofSigmaAndVector 1
AC 4169
S is 1.606348e-24
var1 is 1.968281e-10
p_exact 1
var2sparseGRM Here 1.968281e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4169
var1 1.968281e-10
var2null 1.968281e-10
var2null_noXadj 2.751443e-10
25 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 0 0 0 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
226 22 22_16697442_G_T 0 16697442 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 995
iter from getPCG1ofSigmaAndVector 1
AC 4722
S is 4.25405e-24
var1 is 2.405499e-10
p_exact 1
var2sparseGRM Here 2.4055e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4722
var1 2.405499e-10
var2null 2.405499e-10
var2null_noXadj 3.868031e-10
182 th marker in geno 1
MAC: 34
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1525 22 22_17049480_A_G 0 17049480 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3708
iter from getPCG1ofSigmaAndVector 1
AC 1083
S is 1.803904e-25
var1 is 9.715818e-11
p_exact 1
var2sparseGRM Here 9.715822e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1083
var1 9.715818e-11
var2null 9.715819e-11
var2null_noXadj 1.81562e-10
175 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1479 22 22_17037865_G_T 0 17037865 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -2.610991e-24
var1 is 1.303817e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.303817e-10
var2null 1.303817e-10
var2null_noXadj 2.211101e-10
85 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
629 22 22_16825380_G_A 0 16825380 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2017
iter from getPCG1ofSigmaAndVector 1
AC 3372
S is -1.03857e-24
var1 is 2.609921e-10
p_exact 1
var2sparseGRM Here 2.609921e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3372
var1 2.609921e-10
var2null 2.609921e-10
var2null_noXadj 4.353054e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609
CV for variance ratio estimate using 90 markers is 0.001388658 > 0.001
try 100 markers
57 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
470 22 22_16785735_A_C 0 16785735 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
86 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
630 22 22_16826051_T_TAAC 0 16826051 T TAAC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1281
iter from getPCG1ofSigmaAndVector 1
AC 4596
S is 3.209919e-24
var1 is 2.792824e-10
p_exact 1
var2sparseGRM Here 2.792825e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4596
var1 2.792824e-10
var2null 2.792825e-10
var2null_noXadj 4.687222e-10
482 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3961 22 22_17519297_T_G 0 17519297 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
205 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1706 22 22_17100141_TAA_T 0 17100141 TAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3757
iter from getPCG1ofSigmaAndVector 1
AC 1067
S is 3.586525e-25
var1 is 1.225337e-10
p_exact 1
var2sparseGRM Here 1.225338e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1067
var1 1.225337e-10
var2null 1.225337e-10
var2null_noXadj 1.810654e-10
240 th marker in geno 1
MAC: 65
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 2 1 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
1915 22 22_17137274_C_G 0 17137274 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2388
iter from getPCG1ofSigmaAndVector 1
AC 2572
S is 2.21545e-24
var1 is 1.940903e-10
p_exact 1
var2sparseGRM Here 1.940903e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2572
var1 1.940903e-10
var2null 1.940903e-10
var2null_noXadj 3.092207e-10
148 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 0 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1078 22 22_16947190_T_C 0 16947190 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1816
iter from getPCG1ofSigmaAndVector 1
AC 3745
S is -4.252755e-24
var1 is 2.582015e-10
p_exact 1
var2sparseGRM Here 2.582015e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3745
var1 2.582015e-10
var2null 2.582015e-10
var2null_noXadj 4.689406e-10
484 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3973 22 22_17521351_T_A 0 17521351 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2675
iter from getPCG1ofSigmaAndVector 1
AC 2326
S is -1.754212e-24
var1 is 1.584588e-10
p_exact 1
var2sparseGRM Here 1.584588e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2326
var1 1.584588e-10
var2null 1.584588e-10
var2null_noXadj 3.224383e-10
141 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 1 1 0 2 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1005 22 22_16931326_A_G 0 16931326 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2126
iter from getPCG1ofSigmaAndVector 1
AC 3016
S is -2.314631e-24
var1 is 2.449201e-10
p_exact 1
var2sparseGRM Here 2.449202e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3016
var1 2.449201e-10
var2null 2.449201e-10
var2null_noXadj 3.529569e-10
56 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
457 22 22_16781299_C_T 0 16781299 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
363 th marker in geno 1
MAC: 89
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2808 22 22_17303033_G_A 0 17303033 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1463
iter from getPCG1ofSigmaAndVector 1
AC 4385
S is -4.3843e-25
var1 is 2.645537e-10
p_exact 1
var2sparseGRM Here 2.645538e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4385
var1 2.645537e-10
var2null 2.645537e-10
var2null_noXadj 4.747337e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676
CV for variance ratio estimate using 100 markers is 0.001248106 > 0.001
try 110 markers
91 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
671 22 22_16836343_A_C 0 16836343 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3657
iter from getPCG1ofSigmaAndVector 1
AC 1369
S is 3.350702e-25
var1 is 2.058348e-10
p_exact 1
var2sparseGRM Here 2.058349e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1369
var1 2.058348e-10
var2null 2.058348e-10
var2null_noXadj 2.979653e-10
344 th marker in geno 1
MAC: 29
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2642 22 22_17250567_T_TAAAATAA 0 17250567 T TAAAATAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3561
iter from getPCG1ofSigmaAndVector 1
AC 1293
S is -5.852391e-25
var1 is 1.357912e-10
p_exact 1
var2sparseGRM Here 1.357912e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1293
var1 1.357912e-10
var2null 1.357912e-10
var2null_noXadj 2.144203e-10
253 th marker in geno 1
MAC: 48
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2036 22 22_17161022_A_G 0 17161022 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2814
iter from getPCG1ofSigmaAndVector 1
AC 2574
S is -3.580696e-24
var1 is 3.388007e-10
p_exact 1
var2sparseGRM Here 3.388009e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2574
var1 3.388007e-10
var2null 3.388007e-10
var2null_noXadj 4.617044e-10
322 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2485 22 22_17221690_T_C 0 17221690 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2859
iter from getPCG1ofSigmaAndVector 1
AC 2810
S is 5.546513e-25
var1 is 2.895086e-10
p_exact 1
var2sparseGRM Here 2.895089e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2810
var1 2.895086e-10
var2null 2.895087e-10
var2null_noXadj 5.988163e-10
438 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3507 22 22_17441603_A_AC 0 17441603 A AC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
518 th marker in geno 1
MAC: 77
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4231 22 22_17572793_C_T 0 17572793 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2124
iter from getPCG1ofSigmaAndVector 1
AC 3558
S is -4.092535e-24
var1 is 3.015379e-10
p_exact 1
var2sparseGRM Here 3.01538e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3558
var1 3.015379e-10
var2null 3.015379e-10
var2null_noXadj 5.179161e-10
52 th marker in geno 1
MAC: 51
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
449 22 22_16769333_T_C 0 16769333 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2289
iter from getPCG1ofSigmaAndVector 1
AC 2731
S is -7.096214e-25
var1 is 2.152456e-10
p_exact 1
var2sparseGRM Here 2.152457e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2731
var1 2.152456e-10
var2null 2.152456e-10
var2null_noXadj 3.225962e-10
195 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1607 22 22_17066270_C_A 0 17066270 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2952
iter from getPCG1ofSigmaAndVector 1
AC 2155
S is -1.796378e-24
var1 is 2.287538e-10
p_exact 1
var2sparseGRM Here 2.287539e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2155
var1 2.287538e-10
var2null 2.287538e-10
var2null_noXadj 3.594958e-10
504 th marker in geno 1
MAC: 82
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
4156 22 22_17556556_G_A 0 17556556 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1761
iter from getPCG1ofSigmaAndVector 1
AC 4013
S is 6.219506e-25
var1 is 2.765841e-10
p_exact 1
var2sparseGRM Here 2.765843e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4013
var1 2.765841e-10
var2null 2.765842e-10
var2null_noXadj 5.008253e-10
204 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 1 2 1 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1685 22 22_17092382_A_G 0 17092382 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1299
iter from getPCG1ofSigmaAndVector 1
AC 4568
S is -4.213742e-24
var1 is 2.015821e-10
p_exact 1
var2sparseGRM Here 2.015822e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4568
var1 2.015821e-10
var2null 2.015821e-10
var2null_noXadj 4.535953e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096
CV for variance ratio estimate using 110 markers is 0.001151453 > 0.001
try 120 markers
515 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
4216 22 22_17570663_A_G 0 17570663 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2428
iter from getPCG1ofSigmaAndVector 1
AC 2762
S is -4.176293e-24
var1 is 1.689767e-10
p_exact 1
var2sparseGRM Here 1.689768e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2762
var1 1.689767e-10
var2null 1.689767e-10
var2null_noXadj 3.839481e-10
44 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
362 22 22_16743136_G_A 0 16743136 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3158
iter from getPCG1ofSigmaAndVector 1
AC 1778
S is -5.863572e-25
var1 is 2.020268e-10
p_exact 1
var2sparseGRM Here 2.02027e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1778
var1 2.020268e-10
var2null 2.020268e-10
var2null_noXadj 2.794007e-10
286 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 2 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2276 22 22_17188516_G_C 0 17188516 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2273
iter from getPCG1ofSigmaAndVector 1
AC 3373
S is -3.717466e-24
var1 is 2.827461e-10
p_exact 1
var2sparseGRM Here 2.827462e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3373
var1 2.827461e-10
var2null 2.827461e-10
var2null_noXadj 5.229961e-10
213 th marker in geno 1
MAC: 63
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
1732 22 22_17106856_GGGC_G 0 17106856 GGGC G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2864
iter from getPCG1ofSigmaAndVector 1
AC 2181
S is -1.956375e-25
var1 is 2.37367e-10
p_exact 1
var2sparseGRM Here 2.373671e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2181
var1 2.37367e-10
var2null 2.37367e-10
var2null_noXadj 3.631997e-10
93 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
681 22 22_16839471_A_T 0 16839471 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1534
iter from getPCG1ofSigmaAndVector 1
AC 3866
S is -1.413437e-24
var1 is 2.545011e-10
p_exact 1
var2sparseGRM Here 2.545012e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3866
var1 2.545011e-10
var2null 2.545011e-10
var2null_noXadj 3.785768e-10
59 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
481 22 22_16790535_G_A 0 16790535 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -3.386725e-24
var1 is 1.38251e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.38251e-10
var2null 1.38251e-10
var2null_noXadj 2.290779e-10
256 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2062 22 22_17166972_T_G 0 17166972 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3155
iter from getPCG1ofSigmaAndVector 1
AC 2155
S is -9.513726e-25
var1 is 2.926539e-10
p_exact 1
var2sparseGRM Here 2.926541e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2155
var1 2.926539e-10
var2null 2.92654e-10
var2null_noXadj 4.305838e-10
346 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2657 22 22_17251532_C_CA 0 17251532 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3278
iter from getPCG1ofSigmaAndVector 1
AC 1612
S is -4.940163e-25
var1 is 1.79778e-10
p_exact 1
var2sparseGRM Here 1.797781e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1612
var1 1.79778e-10
var2null 1.79778e-10
var2null_noXadj 2.506762e-10
335 th marker in geno 1
MAC: 66
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 2 0 1 1 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
2588 22 22_17243159_C_A 0 17243159 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2308
iter from getPCG1ofSigmaAndVector 1
AC 2896
S is -1.710023e-24
var1 is 2.438792e-10
p_exact 1
var2sparseGRM Here 2.438794e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2896
var1 2.438792e-10
var2null 2.438792e-10
var2null_noXadj 3.856526e-10
109 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
801 22 22_16864232_G_A 0 16864232 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3653
iter from getPCG1ofSigmaAndVector 1
AC 1185
S is -7.237325e-26
var1 is 1.148315e-10
p_exact 1
var2sparseGRM Here 1.148315e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1185
var1 1.148315e-10
var2null 1.148315e-10
var2null_noXadj 2.012894e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[120] 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096 0.4401030 0.7230721
[113] 0.5406275 0.6535440 0.6722575 0.6035108 0.6796677 0.7171722 0.6323806
[120] 0.5704797
CV for variance ratio estimate using 120 markers is 0.001060431 > 0.001
try 130 markers
442 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 0 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3521 22 22_17443691_C_T 0 17443691 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3391
iter from getPCG1ofSigmaAndVector 1
AC 1843
S is 6.739523e-25
var1 is 2.373953e-10
p_exact 1
var2sparseGRM Here 2.373954e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1843
var1 2.373953e-10
var2null 2.373953e-10
var2null_noXadj 3.921551e-10
203 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 2 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1679 22 22_17090465_G_A 0 17090465 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2267
iter from getPCG1ofSigmaAndVector 1
AC 3285
S is -2.134393e-24
var1 is 3.340378e-10
p_exact 1
var2sparseGRM Here 3.34038e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3285
var1 3.340378e-10
var2null 3.340378e-10
var2null_noXadj 4.901084e-10
392 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 1 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3032 22 22_17352210_T_C 0 17352210 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1392
iter from getPCG1ofSigmaAndVector 1
AC 4581
S is 6.121056e-24
var1 is 3.073406e-10
p_exact 1
var2sparseGRM Here 3.073408e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4581
var1 3.073406e-10
var2null 3.073406e-10
var2null_noXadj 4.9917e-10
294 th marker in geno 1
MAC: 98
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 2 2 1 2 1 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2319 22 22_17196809_C_T 0 17196809 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1757
iter from getPCG1ofSigmaAndVector 1
AC 3747
S is 8.885729e-27
var1 is 2.204993e-10
p_exact 1
var2sparseGRM Here 2.204995e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3747
var1 2.204993e-10
var2null 2.204993e-10
var2null_noXadj 4.569122e-10
154 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1100 22 22_16954034_G_C 0 16954034 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2286
iter from getPCG1ofSigmaAndVector 1
AC 2716
S is -6.334364e-25
var1 is 1.815757e-10
p_exact 1
var2sparseGRM Here 1.815757e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2716
var1 1.815757e-10
var2null 1.815757e-10
var2null_noXadj 3.117158e-10
80 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
612 22 22_16822150_T_C 0 16822150 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2017
iter from getPCG1ofSigmaAndVector 1
AC 3372
S is -1.03857e-24
var1 is 2.609921e-10
p_exact 1
var2sparseGRM Here 2.609921e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3372
var1 2.609921e-10
var2null 2.609921e-10
var2null_noXadj 4.353054e-10
243 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1948 22 22_17145775_T_C 0 17145775 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3327
iter from getPCG1ofSigmaAndVector 1
AC 1541
S is 1.019234e-24
var1 is 1.184986e-10
p_exact 1
var2sparseGRM Here 1.184987e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1541
var1 1.184986e-10
var2null 1.184987e-10
var2null_noXadj 2.378183e-10
296 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2323 22 22_17197269_C_CT 0 17197269 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3249
iter from getPCG1ofSigmaAndVector 1
AC 1605
S is -1.804802e-24
var1 is 1.691563e-10
p_exact 1
var2sparseGRM Here 1.691565e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1605
var1 1.691563e-10
var2null 1.691564e-10
var2null_noXadj 2.386271e-10
35 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 1 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
294 22 22_16724268_T_C 0 16724268 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3558
iter from getPCG1ofSigmaAndVector 1
AC 1270
S is 1.621254e-24
var1 is 1.295267e-10
p_exact 1
var2sparseGRM Here 1.295268e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1270
var1 1.295267e-10
var2null 1.295267e-10
var2null_noXadj 2.022097e-10
100 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
743 22 22_16851949_G_A 0 16851949 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1548
iter from getPCG1ofSigmaAndVector 1
AC 3852
S is -1.19253e-24
var1 is 2.561159e-10
p_exact 1
var2sparseGRM Here 2.561161e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3852
var1 2.561159e-10
var2null 2.561159e-10
var2null_noXadj 3.799173e-10
[1] "varRatio_NULL_vec"
[1] 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999997 1.0000000 0.9999999 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[29] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[36] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000
[43] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 0.9999999
[57] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[64] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[78] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[99] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999996 1.0000000
[106] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 1.0000000 1.0000000
[113] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[120] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[127] 0.9999997 1.0000000 1.0000000 0.9999998
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7291408 0.6741359 0.7230721 0.4772720 0.5820921 0.5896686 0.6326224
[8] 0.6158296 0.4914390 0.7028778 0.5572921 0.5567644 0.5889313 0.5179156
[15] 0.5772228 0.6905119 0.5300961 0.4883599 0.6053607 0.6234838 0.4476232
[22] 0.6901689 0.5969617 0.6053607 0.7365941 0.6311216 0.6406014 0.6607678
[29] 0.5978441 0.6808229 0.6808229 0.7575674 0.6115401 0.6715148 0.5740263
[36] 0.6598067 0.5836401 0.4883599 0.6250143 0.7254755 0.6910274 0.6893129
[43] 0.6445333 0.5811068 0.6275950 0.7947091 0.6140840 0.6479075 0.6008026
[50] 0.5892364 0.7085970 0.6311216 0.5896686 0.6099276 0.5136941 0.6150313
[57] 0.5903726 0.7741352 0.5896686 0.5943514 0.6406014 0.5084634 0.5668018
[64] 0.7804263 0.7753329 0.6157032 0.7743967 0.6962383 0.6405563 0.4772720
[71] 0.4772720 0.6663240 0.6290105 0.6075671 0.6180431 0.6445333 0.5289218
[78] 0.6510286 0.6660976 0.4554597 0.6147501 0.6053607 0.7061542 0.7085970
[85] 0.6451535 0.7153633 0.6218924 0.5351240 0.5896686 0.5995609 0.6035108
[92] 0.5958378 0.4914390 0.6767374 0.6276756 0.5506059 0.4914390 0.6939092
[99] 0.6035108 0.5572676 0.6908012 0.6332943 0.7338045 0.4834681 0.6053607
[106] 0.5822138 0.6672293 0.6363184 0.5522567 0.4444096 0.4401030 0.7230721
[113] 0.5406275 0.6535440 0.6722575 0.6035108 0.6796677 0.7171722 0.6323806
[120] 0.5704797 0.6053607 0.6815590 0.6157032 0.4825858 0.5825038 0.5995609
[127] 0.4982739 0.7088730 0.6405563 0.6741359
CV for variance ratio estimate using 130 markers is 0.0009729458 < 0.001
varRatio_sparseGRM_vec
[1] 0.9999991 0.9999992 0.9999992 0.9999996 0.9999997 0.9999996 0.9999993
[8] 0.9999996 0.9999996 0.9999994 0.9999994 0.9999992 0.9999997 0.9999996
[15] 0.9999996 0.9999997 0.9999997 0.9999995 0.9999995 0.9999998 0.9999997
[22] 0.9999997 0.9999998 0.9999995 0.9999993 0.9999998 0.9999995 0.9999993
[29] 0.9999995 0.9999996 0.9999996 0.9999990 0.9999995 0.9999996 0.9999999
[36] 0.9999994 0.9999996 0.9999995 0.9999994 0.9999995 0.9999998 0.9999997
[43] 0.9999996 0.9999995 0.9999995 0.9999992 0.9999998 0.9999997 0.9999994
[50] 0.9999994 0.9999995 0.9999998 0.9999996 0.9999993 0.9999993 0.9999996
[57] 0.9999999 0.9999996 0.9999996 0.9999998 0.9999995 0.9999997 0.9999995
[64] 0.9999995 0.9999991 0.9999991 1.0000000 0.9999996 0.9999995 0.9999996
[71] 0.9999996 0.9999990 0.9999995 0.9999992 0.9999993 0.9999996 0.9999997
[78] 0.9999999 0.9999998 0.9999997 0.9999994 0.9999995 0.9999994 0.9999995
[85] 0.9999994 0.9999999 0.9999994 0.9999996 0.9999996 0.9999999 0.9999994
[92] 0.9999995 0.9999996 0.9999998 0.9999998 0.9999997 0.9999996 0.9999995
[99] 0.9999994 0.9999997 0.9999995 0.9999995 0.9999993 0.9999990 0.9999995
[106] 0.9999996 0.9999995 0.9999995 0.9999995 0.9999996 0.9999996 0.9999992
[113] 0.9999996 0.9999997 0.9999994 0.9999994 0.9999994 0.9999996 0.9999993
[120] 0.9999998 0.9999995 0.9999993 0.9999991 0.9999993 0.9999995 0.9999999
[127] 0.9999993 0.9999993 0.9999995 0.9999992
varRatio_sparse 0.9999995
varRatio_null 0.9999999
varRatio_null_noXadj 0.6178561
V1 V2 V3
1 0.9999995 sparse 1
2 0.9999999 null 1
3 0.6178561 null_noXadj 1
4 0.9999999 null_sample 1
[2026-01-09 01:40:24,145] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: optparse
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: RhpcBLASctl
warning: solve(): system is singular; attempting approx solution
Loading required package: fastSave
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
3: glm.fit: algorithm did not converge
{'model_file': 'gene1_step1.rda', 'variance_ratio': 0 1 2
0 1.000000 sparse 1
1 1.000000 NaN 1
2 0.617856 null_noXadj 1
3 1.000000 null_sample 1}
Step 2 Only: Association Testing#
step2_results = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="gene1_step1", # Use same prefix as Step 1
steps=[2], # Only Step 2
mode="cis",
window=cis_window,
min_mac=20,
gmmat_model_file="gene1_step1.rda", # From Step 1
variance_ratio_file="gene1_step1.varianceRatio.txt", # From Step 1
run=True,
)
step2_results.head()
Writing FAM... done.
Writing BIM... done.
[2026-01-09 01:40:25,065] INFO:cellink.tl.external._saigeqtl: Running Step 2: Association tests
[2026-01-09 01:40:25,066] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step2_tests_qtl.R --bedFile=gene1_step1.bed --bimFile=gene1_step1.bim --famFile=gene1_step1.fam --GMMATmodelFile=gene1_step1.rda --varianceRatioFile=gene1_step1.varianceRatio.txt --SAIGEOutputFile=gene1_step1_results.txt --minMAC=20 --LOCO=FALSE --rangestoIncludeFile=gene1_step1_ranges.txt
[2026-01-09 01:40:40,849] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.17.6 optparse_1.7.5 RhpcBLASctl_0.23-42
[4] SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] RcppParallel_5.1.9 lattice_0.22-7
$vcfFile
[1] ""
$vcfFileIndex
[1] ""
$vcfField
[1] "DS"
$savFile
[1] ""
$savFileIndex
[1] ""
$bgenFile
[1] ""
$bgenFileIndex
[1] ""
$sampleFile
[1] ""
$bedFile
[1] "gene1_step1.bed"
$bimFile
[1] "gene1_step1.bim"
$famFile
[1] "gene1_step1.fam"
$AlleleOrder
[1] "alt-first"
$idstoIncludeFile
[1] ""
$rangestoIncludeFile
[1] "gene1_step1_ranges.txt"
$chrom
[1] ""
$is_imputed_data
[1] FALSE
$minMAF
[1] 0
$minMAC
[1] 20
$minGroupMAC_in_BurdenTest
[1] 5
$minInfo
[1] 0
$maxMissing
[1] 0.15
$impute_method
[1] "best_guess"
$LOCO
[1] FALSE
$GMMATmodelFile
[1] "gene1_step1.rda"
$varianceRatioFile
[1] "gene1_step1.varianceRatio.txt"
$GMMATmodel_varianceRatio_multiTraits_File
[1] ""
$SAIGEOutputFile
[1] "gene1_step1_results.txt"
$markers_per_chunk
[1] 10000
$groups_per_chunk
[1] 100
$is_output_moreDetails
[1] FALSE
$is_overwrite_output
[1] TRUE
$maxMAF_in_groupTest
[1] "0.0001,0.001,0.01"
$maxMAC_in_groupTest
[1] "0"
$annotation_in_groupTest
[1] "lof,missense;lof,missense;lof;synonymous"
$groupFile
[1] ""
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$relatednessCutoff
[1] 0
$MACCutoff_to_CollapseUltraRare
[1] 10
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$weights.beta
[1] "1;25"
$r.corr
[1] 0
$markers_per_chunk_in_groupTest
[1] 100
$condition
[1] ""
$SPAcutoff
[1] 2
$dosage_zerod_cutoff
[1] 0.2
$dosage_zerod_MAC_cutoff
[1] 10
$is_single_in_groupTest
[1] FALSE
$is_SKATO
[1] FALSE
$is_equal_weight_in_groupTest
[1] FALSE
$is_output_markerList_in_groupTest
[1] FALSE
$is_Firth_beta
[1] FALSE
$pCutoffforFirth
[1] 0.01
$is_fastTest
[1] FALSE
$is_noadjCov
[1] TRUE
$is_sparseGRM
[1] FALSE
$pval_cutoff_for_fastTest
[1] 0.05
$max_MAC_for_ER
[1] 4
$is_EmpSPA
[1] FALSE
$help
[1] FALSE
[1] "opt$r.corr"
[1] 0
dosage_zerod_cutoff 0.2
Any dosages <= 0.2 for genetic variants with MAC <= 10 are set to be 0 in group tests
single-variant association test will be performed
[1] "Leave-one-chromosome-out is not applied"
[1] "LOCO = FASLE and leave-one-chromosome-out is not applied"
isSparseGRM FALSE
variance Ratio null is 0.9999999
variance Ratio null_noXadj is 0.6178561
variance Ratio ratioVec_null_sample is 0.9999999
$ratioVec_sparse
[1] 0.9999995
$ratioVec_null
[1] 0.9999999
$ratioVec_null_sample
[1] 0.9999999
$ratioVec_null_noXadj
[1] 0.6178561
$ratioVec_null_eg
[1] -1
$ratioVec_sparse_eg
[1] -1
dosageFile type is plink
allele order in the plink file is alt-first .
Reading bim file....
Reading fam file....
Setting position of samples in PLINK files....
871 ranges are in rangestoIncludeFile
22 markers in the range 1 are found in the geno/dosage file.
1422 markers in the range 2 are found in the geno/dosage file.
1686 markers in the range 3 are found in the geno/dosage file.
1705 markers in the range 4 are found in the geno/dosage file.
1784 markers in the range 5 are found in the geno/dosage file.
2156 markers in the range 6 are found in the geno/dosage file.
2627 markers in the range 7 are found in the geno/dosage file.
2632 markers in the range 8 are found in the geno/dosage file.
2931 markers in the range 9 are found in the geno/dosage file.
3109 markers in the range 10 are found in the geno/dosage file.
3224 markers in the range 11 are found in the geno/dosage file.
3270 markers in the range 12 are found in the geno/dosage file.
3312 markers in the range 13 are found in the geno/dosage file.
3350 markers in the range 14 are found in the geno/dosage file.
3433 markers in the range 15 are found in the geno/dosage file.
3880 markers in the range 16 are found in the geno/dosage file.
4200 markers in the range 17 are found in the geno/dosage file.
4194 markers in the range 18 are found in the geno/dosage file.
4151 markers in the range 19 are found in the geno/dosage file.
4151 markers in the range 20 are found in the geno/dosage file.
4147 markers in the range 21 are found in the geno/dosage file.
4128 markers in the range 22 are found in the geno/dosage file.
4112 markers in the range 23 are found in the geno/dosage file.
3865 markers in the range 24 are found in the geno/dosage file.
3498 markers in the range 25 are found in the geno/dosage file.
2883 markers in the range 26 are found in the geno/dosage file.
2677 markers in the range 27 are found in the geno/dosage file.
2638 markers in the range 28 are found in the geno/dosage file.
2593 markers in the range 29 are found in the geno/dosage file.
2437 markers in the range 30 are found in the geno/dosage file.
1734 markers in the range 31 are found in the geno/dosage file.
1532 markers in the range 32 are found in the geno/dosage file.
1501 markers in the range 33 are found in the geno/dosage file.
1484 markers in the range 34 are found in the geno/dosage file.
492 markers in the range 35 are found in the geno/dosage file.
395 markers in the range 36 are found in the geno/dosage file.
256 markers in the range 37 are found in the geno/dosage file.
33 markers in the range 38 are found in the geno/dosage file.
17 markers in the range 39 are found in the geno/dosage file.
0 markers in the range 40 are found in the geno/dosage file.
0 markers in the range 41 are found in the geno/dosage file.
0 markers in the range 42 are found in the geno/dosage file.
0 markers in the range 43 are found in the geno/dosage file.
0 markers in the range 44 are found in the geno/dosage file.
0 markers in the range 45 are found in the geno/dosage file.
0 markers in the range 46 are found in the geno/dosage file.
0 markers in the range 47 are found in the geno/dosage file.
0 markers in the range 48 are found in the geno/dosage file.
0 markers in the range 49 are found in the geno/dosage file.
0 markers in the range 50 are found in the geno/dosage file.
0 markers in the range 51 are found in the geno/dosage file.
0 markers in the range 52 are found in the geno/dosage file.
0 markers in the range 53 are found in the geno/dosage file.
0 markers in the range 54 are found in the geno/dosage file.
0 markers in the range 55 are found in the geno/dosage file.
0 markers in the range 56 are found in the geno/dosage file.
0 markers in the range 57 are found in the geno/dosage file.
0 markers in the range 58 are found in the geno/dosage file.
0 markers in the range 59 are found in the geno/dosage file.
0 markers in the range 60 are found in the geno/dosage file.
0 markers in the range 61 are found in the geno/dosage file.
0 markers in the range 62 are found in the geno/dosage file.
0 markers in the range 63 are found in the geno/dosage file.
0 markers in the range 64 are found in the geno/dosage file.
0 markers in the range 65 are found in the geno/dosage file.
0 markers in the range 66 are found in the geno/dosage file.
0 markers in the range 67 are found in the geno/dosage file.
0 markers in the range 68 are found in the geno/dosage file.
0 markers in the range 69 are found in the geno/dosage file.
0 markers in the range 70 are found in the geno/dosage file.
0 markers in the range 71 are found in the geno/dosage file.
0 markers in the range 72 are found in the geno/dosage file.
0 markers in the range 73 are found in the geno/dosage file.
0 markers in the range 74 are found in the geno/dosage file.
0 markers in the range 75 are found in the geno/dosage file.
0 markers in the range 76 are found in the geno/dosage file.
0 markers in the range 77 are found in the geno/dosage file.
0 markers in the range 78 are found in the geno/dosage file.
0 markers in the range 79 are found in the geno/dosage file.
0 markers in the range 80 are found in the geno/dosage file.
0 markers in the range 81 are found in the geno/dosage file.
0 markers in the range 82 are found in the geno/dosage file.
0 markers in the range 83 are found in the geno/dosage file.
0 markers in the range 84 are found in the geno/dosage file.
0 markers in the range 85 are found in the geno/dosage file.
0 markers in the range 86 are found in the geno/dosage file.
0 markers in the range 87 are found in the geno/dosage file.
0 markers in the range 88 are found in the geno/dosage file.
0 markers in the range 89 are found in the geno/dosage file.
0 markers in the range 90 are found in the geno/dosage file.
0 markers in the range 91 are found in the geno/dosage file.
0 markers in the range 92 are found in the geno/dosage file.
0 markers in the range 93 are found in the geno/dosage file.
0 markers in the range 94 are found in the geno/dosage file.
0 markers in the range 95 are found in the geno/dosage file.
0 markers in the range 96 are found in the geno/dosage file.
0 markers in the range 97 are found in the geno/dosage file.
0 markers in the range 98 are found in the geno/dosage file.
0 markers in the range 99 are found in the geno/dosage file.
0 markers in the range 100 are found in the geno/dosage file.
0 markers in the range 101 are found in the geno/dosage file.
0 markers in the range 102 are found in the geno/dosage file.
0 markers in the range 103 are found in the geno/dosage file.
0 markers in the range 104 are found in the geno/dosage file.
0 markers in the range 105 are found in the geno/dosage file.
0 markers in the range 106 are found in the geno/dosage file.
0 markers in the range 107 are found in the geno/dosage file.
0 markers in the range 108 are found in the geno/dosage file.
0 markers in the range 109 are found in the geno/dosage file.
0 markers in the range 110 are found in the geno/dosage file.
0 markers in the range 111 are found in the geno/dosage file.
0 markers in the range 112 are found in the geno/dosage file.
0 markers in the range 113 are found in the geno/dosage file.
0 markers in the range 114 are found in the geno/dosage file.
0 markers in the range 115 are found in the geno/dosage file.
0 markers in the range 116 are found in the geno/dosage file.
0 markers in the range 117 are found in the geno/dosage file.
0 markers in the range 118 are found in the geno/dosage file.
0 markers in the range 119 are found in the geno/dosage file.
0 markers in the range 120 are found in the geno/dosage file.
0 markers in the range 121 are found in the geno/dosage file.
0 markers in the range 122 are found in the geno/dosage file.
0 markers in the range 123 are found in the geno/dosage file.
0 markers in the range 124 are found in the geno/dosage file.
0 markers in the range 125 are found in the geno/dosage file.
0 markers in the range 126 are found in the geno/dosage file.
0 markers in the range 127 are found in the geno/dosage file.
0 markers in the range 128 are found in the geno/dosage file.
0 markers in the range 129 are found in the geno/dosage file.
0 markers in the range 130 are found in the geno/dosage file.
0 markers in the range 131 are found in the geno/dosage file.
0 markers in the range 132 are found in the geno/dosage file.
0 markers in the range 133 are found in the geno/dosage file.
0 markers in the range 134 are found in the geno/dosage file.
0 markers in the range 135 are found in the geno/dosage file.
0 markers in the range 136 are found in the geno/dosage file.
0 markers in the range 137 are found in the geno/dosage file.
0 markers in the range 138 are found in the geno/dosage file.
0 markers in the range 139 are found in the geno/dosage file.
0 markers in the range 140 are found in the geno/dosage file.
0 markers in the range 141 are found in the geno/dosage file.
0 markers in the range 142 are found in the geno/dosage file.
0 markers in the range 143 are found in the geno/dosage file.
0 markers in the range 144 are found in the geno/dosage file.
0 markers in the range 145 are found in the geno/dosage file.
0 markers in the range 146 are found in the geno/dosage file.
0 markers in the range 147 are found in the geno/dosage file.
0 markers in the range 148 are found in the geno/dosage file.
0 markers in the range 149 are found in the geno/dosage file.
0 markers in the range 150 are found in the geno/dosage file.
0 markers in the range 151 are found in the geno/dosage file.
0 markers in the range 152 are found in the geno/dosage file.
0 markers in the range 153 are found in the geno/dosage file.
0 markers in the range 154 are found in the geno/dosage file.
0 markers in the range 155 are found in the geno/dosage file.
0 markers in the range 156 are found in the geno/dosage file.
0 markers in the range 157 are found in the geno/dosage file.
0 markers in the range 158 are found in the geno/dosage file.
0 markers in the range 159 are found in the geno/dosage file.
0 markers in the range 160 are found in the geno/dosage file.
0 markers in the range 161 are found in the geno/dosage file.
0 markers in the range 162 are found in the geno/dosage file.
0 markers in the range 163 are found in the geno/dosage file.
0 markers in the range 164 are found in the geno/dosage file.
0 markers in the range 165 are found in the geno/dosage file.
0 markers in the range 166 are found in the geno/dosage file.
0 markers in the range 167 are found in the geno/dosage file.
0 markers in the range 168 are found in the geno/dosage file.
0 markers in the range 169 are found in the geno/dosage file.
0 markers in the range 170 are found in the geno/dosage file.
0 markers in the range 171 are found in the geno/dosage file.
0 markers in the range 172 are found in the geno/dosage file.
0 markers in the range 173 are found in the geno/dosage file.
0 markers in the range 174 are found in the geno/dosage file.
0 markers in the range 175 are found in the geno/dosage file.
0 markers in the range 176 are found in the geno/dosage file.
0 markers in the range 177 are found in the geno/dosage file.
0 markers in the range 178 are found in the geno/dosage file.
0 markers in the range 179 are found in the geno/dosage file.
0 markers in the range 180 are found in the geno/dosage file.
0 markers in the range 181 are found in the geno/dosage file.
0 markers in the range 182 are found in the geno/dosage file.
0 markers in the range 183 are found in the geno/dosage file.
0 markers in the range 184 are found in the geno/dosage file.
0 markers in the range 185 are found in the geno/dosage file.
0 markers in the range 186 are found in the geno/dosage file.
0 markers in the range 187 are found in the geno/dosage file.
0 markers in the range 188 are found in the geno/dosage file.
0 markers in the range 189 are found in the geno/dosage file.
0 markers in the range 190 are found in the geno/dosage file.
0 markers in the range 191 are found in the geno/dosage file.
0 markers in the range 192 are found in the geno/dosage file.
0 markers in the range 193 are found in the geno/dosage file.
0 markers in the range 194 are found in the geno/dosage file.
0 markers in the range 195 are found in the geno/dosage file.
0 markers in the range 196 are found in the geno/dosage file.
0 markers in the range 197 are found in the geno/dosage file.
0 markers in the range 198 are found in the geno/dosage file.
0 markers in the range 199 are found in the geno/dosage file.
0 markers in the range 200 are found in the geno/dosage file.
0 markers in the range 201 are found in the geno/dosage file.
0 markers in the range 202 are found in the geno/dosage file.
0 markers in the range 203 are found in the geno/dosage file.
0 markers in the range 204 are found in the geno/dosage file.
0 markers in the range 205 are found in the geno/dosage file.
0 markers in the range 206 are found in the geno/dosage file.
0 markers in the range 207 are found in the geno/dosage file.
0 markers in the range 208 are found in the geno/dosage file.
0 markers in the range 209 are found in the geno/dosage file.
0 markers in the range 210 are found in the geno/dosage file.
0 markers in the range 211 are found in the geno/dosage file.
0 markers in the range 212 are found in the geno/dosage file.
0 markers in the range 213 are found in the geno/dosage file.
0 markers in the range 214 are found in the geno/dosage file.
0 markers in the range 215 are found in the geno/dosage file.
0 markers in the range 216 are found in the geno/dosage file.
0 markers in the range 217 are found in the geno/dosage file.
0 markers in the range 218 are found in the geno/dosage file.
0 markers in the range 219 are found in the geno/dosage file.
0 markers in the range 220 are found in the geno/dosage file.
0 markers in the range 221 are found in the geno/dosage file.
0 markers in the range 222 are found in the geno/dosage file.
0 markers in the range 223 are found in the geno/dosage file.
0 markers in the range 224 are found in the geno/dosage file.
0 markers in the range 225 are found in the geno/dosage file.
0 markers in the range 226 are found in the geno/dosage file.
0 markers in the range 227 are found in the geno/dosage file.
0 markers in the range 228 are found in the geno/dosage file.
0 markers in the range 229 are found in the geno/dosage file.
0 markers in the range 230 are found in the geno/dosage file.
0 markers in the range 231 are found in the geno/dosage file.
0 markers in the range 232 are found in the geno/dosage file.
0 markers in the range 233 are found in the geno/dosage file.
0 markers in the range 234 are found in the geno/dosage file.
0 markers in the range 235 are found in the geno/dosage file.
0 markers in the range 236 are found in the geno/dosage file.
0 markers in the range 237 are found in the geno/dosage file.
0 markers in the range 238 are found in the geno/dosage file.
0 markers in the range 239 are found in the geno/dosage file.
0 markers in the range 240 are found in the geno/dosage file.
0 markers in the range 241 are found in the geno/dosage file.
0 markers in the range 242 are found in the geno/dosage file.
0 markers in the range 243 are found in the geno/dosage file.
0 markers in the range 244 are found in the geno/dosage file.
0 markers in the range 245 are found in the geno/dosage file.
0 markers in the range 246 are found in the geno/dosage file.
0 markers in the range 247 are found in the geno/dosage file.
0 markers in the range 248 are found in the geno/dosage file.
0 markers in the range 249 are found in the geno/dosage file.
0 markers in the range 250 are found in the geno/dosage file.
0 markers in the range 251 are found in the geno/dosage file.
0 markers in the range 252 are found in the geno/dosage file.
0 markers in the range 253 are found in the geno/dosage file.
0 markers in the range 254 are found in the geno/dosage file.
0 markers in the range 255 are found in the geno/dosage file.
0 markers in the range 256 are found in the geno/dosage file.
0 markers in the range 257 are found in the geno/dosage file.
0 markers in the range 258 are found in the geno/dosage file.
0 markers in the range 259 are found in the geno/dosage file.
0 markers in the range 260 are found in the geno/dosage file.
0 markers in the range 261 are found in the geno/dosage file.
0 markers in the range 262 are found in the geno/dosage file.
0 markers in the range 263 are found in the geno/dosage file.
0 markers in the range 264 are found in the geno/dosage file.
0 markers in the range 265 are found in the geno/dosage file.
0 markers in the range 266 are found in the geno/dosage file.
0 markers in the range 267 are found in the geno/dosage file.
0 markers in the range 268 are found in the geno/dosage file.
0 markers in the range 269 are found in the geno/dosage file.
0 markers in the range 270 are found in the geno/dosage file.
0 markers in the range 271 are found in the geno/dosage file.
0 markers in the range 272 are found in the geno/dosage file.
0 markers in the range 273 are found in the geno/dosage file.
0 markers in the range 274 are found in the geno/dosage file.
0 markers in the range 275 are found in the geno/dosage file.
0 markers in the range 276 are found in the geno/dosage file.
0 markers in the range 277 are found in the geno/dosage file.
0 markers in the range 278 are found in the geno/dosage file.
0 markers in the range 279 are found in the geno/dosage file.
0 markers in the range 280 are found in the geno/dosage file.
0 markers in the range 281 are found in the geno/dosage file.
0 markers in the range 282 are found in the geno/dosage file.
0 markers in the range 283 are found in the geno/dosage file.
0 markers in the range 284 are found in the geno/dosage file.
0 markers in the range 285 are found in the geno/dosage file.
0 markers in the range 286 are found in the geno/dosage file.
0 markers in the range 287 are found in the geno/dosage file.
0 markers in the range 288 are found in the geno/dosage file.
0 markers in the range 289 are found in the geno/dosage file.
0 markers in the range 290 are found in the geno/dosage file.
0 markers in the range 291 are found in the geno/dosage file.
0 markers in the range 292 are found in the geno/dosage file.
0 markers in the range 293 are found in the geno/dosage file.
0 markers in the range 294 are found in the geno/dosage file.
0 markers in the range 295 are found in the geno/dosage file.
0 markers in the range 296 are found in the geno/dosage file.
0 markers in the range 297 are found in the geno/dosage file.
0 markers in the range 298 are found in the geno/dosage file.
0 markers in the range 299 are found in the geno/dosage file.
0 markers in the range 300 are found in the geno/dosage file.
0 markers in the range 301 are found in the geno/dosage file.
0 markers in the range 302 are found in the geno/dosage file.
0 markers in the range 303 are found in the geno/dosage file.
0 markers in the range 304 are found in the geno/dosage file.
0 markers in the range 305 are found in the geno/dosage file.
0 markers in the range 306 are found in the geno/dosage file.
0 markers in the range 307 are found in the geno/dosage file.
0 markers in the range 308 are found in the geno/dosage file.
0 markers in the range 309 are found in the geno/dosage file.
0 markers in the range 310 are found in the geno/dosage file.
0 markers in the range 311 are found in the geno/dosage file.
0 markers in the range 312 are found in the geno/dosage file.
0 markers in the range 313 are found in the geno/dosage file.
0 markers in the range 314 are found in the geno/dosage file.
0 markers in the range 315 are found in the geno/dosage file.
0 markers in the range 316 are found in the geno/dosage file.
0 markers in the range 317 are found in the geno/dosage file.
0 markers in the range 318 are found in the geno/dosage file.
0 markers in the range 319 are found in the geno/dosage file.
0 markers in the range 320 are found in the geno/dosage file.
0 markers in the range 321 are found in the geno/dosage file.
0 markers in the range 322 are found in the geno/dosage file.
0 markers in the range 323 are found in the geno/dosage file.
0 markers in the range 324 are found in the geno/dosage file.
0 markers in the range 325 are found in the geno/dosage file.
0 markers in the range 326 are found in the geno/dosage file.
0 markers in the range 327 are found in the geno/dosage file.
0 markers in the range 328 are found in the geno/dosage file.
0 markers in the range 329 are found in the geno/dosage file.
0 markers in the range 330 are found in the geno/dosage file.
0 markers in the range 331 are found in the geno/dosage file.
0 markers in the range 332 are found in the geno/dosage file.
0 markers in the range 333 are found in the geno/dosage file.
0 markers in the range 334 are found in the geno/dosage file.
0 markers in the range 335 are found in the geno/dosage file.
0 markers in the range 336 are found in the geno/dosage file.
0 markers in the range 337 are found in the geno/dosage file.
0 markers in the range 338 are found in the geno/dosage file.
0 markers in the range 339 are found in the geno/dosage file.
0 markers in the range 340 are found in the geno/dosage file.
0 markers in the range 341 are found in the geno/dosage file.
0 markers in the range 342 are found in the geno/dosage file.
0 markers in the range 343 are found in the geno/dosage file.
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0 markers in the range 763 are found in the geno/dosage file.
0 markers in the range 764 are found in the geno/dosage file.
0 markers in the range 765 are found in the geno/dosage file.
0 markers in the range 766 are found in the geno/dosage file.
0 markers in the range 767 are found in the geno/dosage file.
0 markers in the range 768 are found in the geno/dosage file.
0 markers in the range 769 are found in the geno/dosage file.
0 markers in the range 770 are found in the geno/dosage file.
0 markers in the range 771 are found in the geno/dosage file.
0 markers in the range 772 are found in the geno/dosage file.
0 markers in the range 773 are found in the geno/dosage file.
0 markers in the range 774 are found in the geno/dosage file.
0 markers in the range 775 are found in the geno/dosage file.
0 markers in the range 776 are found in the geno/dosage file.
0 markers in the range 777 are found in the geno/dosage file.
0 markers in the range 778 are found in the geno/dosage file.
0 markers in the range 779 are found in the geno/dosage file.
0 markers in the range 780 are found in the geno/dosage file.
0 markers in the range 781 are found in the geno/dosage file.
0 markers in the range 782 are found in the geno/dosage file.
0 markers in the range 783 are found in the geno/dosage file.
0 markers in the range 784 are found in the geno/dosage file.
0 markers in the range 785 are found in the geno/dosage file.
0 markers in the range 786 are found in the geno/dosage file.
0 markers in the range 787 are found in the geno/dosage file.
0 markers in the range 788 are found in the geno/dosage file.
0 markers in the range 789 are found in the geno/dosage file.
0 markers in the range 790 are found in the geno/dosage file.
0 markers in the range 791 are found in the geno/dosage file.
0 markers in the range 792 are found in the geno/dosage file.
0 markers in the range 793 are found in the geno/dosage file.
0 markers in the range 794 are found in the geno/dosage file.
0 markers in the range 795 are found in the geno/dosage file.
0 markers in the range 796 are found in the geno/dosage file.
0 markers in the range 797 are found in the geno/dosage file.
0 markers in the range 798 are found in the geno/dosage file.
0 markers in the range 799 are found in the geno/dosage file.
0 markers in the range 800 are found in the geno/dosage file.
0 markers in the range 801 are found in the geno/dosage file.
0 markers in the range 802 are found in the geno/dosage file.
0 markers in the range 803 are found in the geno/dosage file.
0 markers in the range 804 are found in the geno/dosage file.
0 markers in the range 805 are found in the geno/dosage file.
0 markers in the range 806 are found in the geno/dosage file.
0 markers in the range 807 are found in the geno/dosage file.
0 markers in the range 808 are found in the geno/dosage file.
0 markers in the range 809 are found in the geno/dosage file.
0 markers in the range 810 are found in the geno/dosage file.
0 markers in the range 811 are found in the geno/dosage file.
0 markers in the range 812 are found in the geno/dosage file.
0 markers in the range 813 are found in the geno/dosage file.
0 markers in the range 814 are found in the geno/dosage file.
0 markers in the range 815 are found in the geno/dosage file.
0 markers in the range 816 are found in the geno/dosage file.
0 markers in the range 817 are found in the geno/dosage file.
0 markers in the range 818 are found in the geno/dosage file.
0 markers in the range 819 are found in the geno/dosage file.
0 markers in the range 820 are found in the geno/dosage file.
0 markers in the range 821 are found in the geno/dosage file.
0 markers in the range 822 are found in the geno/dosage file.
0 markers in the range 823 are found in the geno/dosage file.
0 markers in the range 824 are found in the geno/dosage file.
0 markers in the range 825 are found in the geno/dosage file.
0 markers in the range 826 are found in the geno/dosage file.
0 markers in the range 827 are found in the geno/dosage file.
0 markers in the range 828 are found in the geno/dosage file.
0 markers in the range 829 are found in the geno/dosage file.
0 markers in the range 830 are found in the geno/dosage file.
0 markers in the range 831 are found in the geno/dosage file.
0 markers in the range 832 are found in the geno/dosage file.
0 markers in the range 833 are found in the geno/dosage file.
0 markers in the range 834 are found in the geno/dosage file.
0 markers in the range 835 are found in the geno/dosage file.
0 markers in the range 836 are found in the geno/dosage file.
0 markers in the range 837 are found in the geno/dosage file.
0 markers in the range 838 are found in the geno/dosage file.
0 markers in the range 839 are found in the geno/dosage file.
0 markers in the range 840 are found in the geno/dosage file.
0 markers in the range 841 are found in the geno/dosage file.
0 markers in the range 842 are found in the geno/dosage file.
0 markers in the range 843 are found in the geno/dosage file.
0 markers in the range 844 are found in the geno/dosage file.
0 markers in the range 845 are found in the geno/dosage file.
0 markers in the range 846 are found in the geno/dosage file.
0 markers in the range 847 are found in the geno/dosage file.
0 markers in the range 848 are found in the geno/dosage file.
0 markers in the range 849 are found in the geno/dosage file.
0 markers in the range 850 are found in the geno/dosage file.
0 markers in the range 851 are found in the geno/dosage file.
0 markers in the range 852 are found in the geno/dosage file.
0 markers in the range 853 are found in the geno/dosage file.
0 markers in the range 854 are found in the geno/dosage file.
0 markers in the range 855 are found in the geno/dosage file.
0 markers in the range 856 are found in the geno/dosage file.
0 markers in the range 857 are found in the geno/dosage file.
0 markers in the range 858 are found in the geno/dosage file.
0 markers in the range 859 are found in the geno/dosage file.
0 markers in the range 860 are found in the geno/dosage file.
0 markers in the range 861 are found in the geno/dosage file.
0 markers in the range 862 are found in the geno/dosage file.
0 markers in the range 863 are found in the geno/dosage file.
0 markers in the range 864 are found in the geno/dosage file.
0 markers in the range 865 are found in the geno/dosage file.
0 markers in the range 866 are found in the geno/dosage file.
0 markers in the range 867 are found in the geno/dosage file.
0 markers in the range 868 are found in the geno/dosage file.
0 markers in the range 869 are found in the geno/dosage file.
0 markers in the range 870 are found in the geno/dosage file.
0 markers in the range 871 are found in the geno/dosage file.
[1] 100 100
isSparseGRM 2 TRUE
pval_cutoff_for_gxe 0.001
traitType count
Number of phenotypes to test: 1
Number of all markers to test: 4277
Number of markers in each chunk: 10000
Number of chunks for all markers: 1
(2026-01-09 00:40:40.59832) ---- Analyzing Chunk 1/1: chrom InitialChunk ----
2433 markers were tested.
write to output
user system elapsed
13.514 1.941 15.327
[1] "Analysis done! The results have been saved to 'gene1_step1_results.txt'."
[2026-01-09 01:40:40,850] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: RhpcBLASctl
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: furrr
Loading required package: future
| CHR | POS | MarkerID | Allele1 | Allele2 | AC_Allele2 | AF_Allele2 | MissingRate | BETA | SE | Tstat | var | p.value | p.value.NA | Is.SPA | N | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 22 | 16569715 | 22_16569715_G_A | A | G | 106 | 0.530 | 0 | 9.658680e-16 | 54135.1 | 3.295800e-25 | 3.412270e-10 | 1 | 1 | False | 100 |
| 1 | 22 | 16569887 | 22_16569887_T_A | A | T | 133 | 0.665 | 0 | 7.073560e-16 | 61436.3 | 1.874080e-25 | 2.649420e-10 | 1 | 1 | False | 100 |
| 2 | 22 | 16570090 | 22_16570090_ACATT_A | A | ACATT | 151 | 0.755 | 0 | 5.051070e-16 | 69893.4 | 1.033980e-25 | 2.047040e-10 | 1 | 1 | False | 100 |
| 3 | 22 | 16570885 | 22_16570885_T_G | G | T | 141 | 0.705 | 0 | 1.208410e-15 | 63757.8 | 2.972680e-25 | 2.459990e-10 | 1 | 1 | False | 100 |
| 4 | 22 | 16571233 | 22_16571233_G_A | A | G | 101 | 0.505 | 0 | 5.824050e-16 | 56733.4 | 1.809460e-25 | 3.106870e-10 | 1 | 1 | False | 100 |
Step 3 Only: Gene-Level P-values#
# Run only Step 3 (requires Step 2 results)
step3_results = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="gene1_step1", # Same prefix
steps=[3], # Only Step 3
gene_name="MYC", # Optional gene name for output
run=True,
)
print(step3_results)
[2026-01-09 01:40:40,873] INFO:cellink.tl.external._saigeqtl: Running Step 3: Gene-level p-values
[2026-01-09 01:40:40,875] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step3_gene_pvalue_qtl.R --assocFile=gene1_step1_results.txt --genePval_outputFile=gene1_step1_gene_pvalue.txt --geneName=MYC
[2026-01-09 01:40:55,516] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.17.6 optparse_1.7.5 RhpcBLASctl_0.23-42
[4] SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] RcppParallel_5.1.9 lattice_0.22-7
$assocFile
[1] "gene1_step1_results.txt"
$weightFile
[1] ""
$geneName
[1] "MYC"
$genePval_outputFile
[1] "gene1_step1_gene_pvalue.txt"
$help
[1] FALSE
MarkerID p.value
<char> <int>
1: 22_16569715_G_A 1
2: 22_16569887_T_A 1
3: 22_16570090_ACATT_A 1
4: 22_16570885_T_G 1
5: 22_16571233_G_A 1
6: 22_16573830_T_C 1
top_MarkerID 22_16569715_G_A
top_pval 1
[2026-01-09 01:40:55,517] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: RhpcBLASctl
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
gene ACAT_p top_MarkerID top_pval
0 MYC 1 22_16569715_G_A 1
2. Advanced: Custom Covariate Specification#
Including cell-type-specific covariates and custom normalizations:
sc.pp.pca(dd.C, n_comps=15)
results_custom = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="saigeqtl_custom",
mode="cis",
window=cis_window,
sample_covariates=["gPCs"],
cell_covariates=["X_pca"],
encode_sex=True,
encode_age=True,
min_mac=20,
use_grm_to_fit_null=False,
overwrite_variance_ratio_file=True,
run=True,
)
results_custom.head()
Writing FAM... done.
Writing BIM... done.
[2026-01-09 01:40:56,880] INFO:cellink.tl.external._saigeqtl: Running Step 1: Fitting null model
[2026-01-09 01:40:56,881] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step1_fitNULLGLMM_qtl.R --phenoFile=saigeqtl_custom_phenotype.txt --phenoCol=ENSG00000273362 --sampleIDColinphenoFile=IND_ID --traitType=count --plinkFile=saigeqtl_custom --outputPrefix=saigeqtl_custom --LOCO=FALSE --useGRMtoFitNULL=FALSE --IsOverwriteVarianceRatioFile=TRUE --covarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19,X_pca_0,X_pca_1,X_pca_2,X_pca_3,X_pca_4,X_pca_5,X_pca_6,X_pca_7,X_pca_8,X_pca_9,X_pca_10,X_pca_11,X_pca_12,X_pca_13,X_pca_14 --sampleCovarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19
[2026-01-09 01:41:14,392] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] optparse_1.7.5 SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] data.table_1.17.6 RcppParallel_5.1.9 lattice_0.22-7
$plinkFile
[1] "saigeqtl_custom"
$bedFile
[1] ""
$bimFile
[1] ""
$famFile
[1] ""
$phenoFile
[1] "saigeqtl_custom_phenotype.txt"
$phenoCol
[1] "ENSG00000273362"
$isRemoveZerosinPheno
[1] FALSE
$traitType
[1] "count"
$invNormalize
[1] FALSE
$covarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19,X_pca_0,X_pca_1,X_pca_2,X_pca_3,X_pca_4,X_pca_5,X_pca_6,X_pca_7,X_pca_8,X_pca_9,X_pca_10,X_pca_11,X_pca_12,X_pca_13,X_pca_14"
$sampleCovarColList
[1] "sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19"
$longlCol
[1] ""
$qCovarColList
[1] ""
$sampleIDColinphenoFile
[1] "IND_ID"
$cellIDColinphenoFile
[1] ""
$tol
[1] 0.02
$maxiter
[1] 20
$tolPCG
[1] 1e-05
$maxiterPCG
[1] 500
$nThreads
[1] 1
$SPAcutoff
[1] 2
$numRandomMarkerforVarianceRatio
[1] 30
$skipModelFitting
[1] FALSE
$skipVarianceRatioEstimation
[1] FALSE
$memoryChunk
[1] 2
$tauInit
[1] "0,0"
$LOCO
[1] FALSE
$isLowMemLOCO
[1] FALSE
$traceCVcutoff
[1] 0.0025
$nrun
[1] 30
$ratioCVcutoff
[1] 0.001
$outputPrefix
[1] "saigeqtl_custom"
$outputPrefix_varRatio
[1] ""
$IsOverwriteVarianceRatioFile
[1] TRUE
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$isCateVarianceRatio
[1] FALSE
$relatednessCutoff
[1] 0
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$isCovariateTransform
[1] TRUE
$isDiagofKinSetAsOne
[1] FALSE
$useSparseGRMtoFitNULL
[1] FALSE
$useSparseGRMforVarRatio
[1] FALSE
$minMAFforGRM
[1] 0.01
$maxMissingRateforGRM
[1] 0.15
$minCovariateCount
[1] -1
$includeNonautoMarkersforVarRatio
[1] FALSE
$FemaleOnly
[1] FALSE
$MaleOnly
[1] FALSE
$sexCol
[1] ""
$FemaleCode
[1] "1"
$MaleCode
[1] "0"
$isCovariateOffset
[1] TRUE
$SampleIDIncludeFile
[1] ""
$VmatFilelist
[1] ""
$VmatSampleFilelist
[1] ""
$useGRMtoFitNULL
[1] FALSE
$isStoreSigma
[1] TRUE
$isShrinkModelOutput
[1] TRUE
$isExportResiduals
[1] FALSE
$help
[1] FALSE
tauInit is 0 0
cateVarRatioMinMACVecExclude is 10 20.5
cateVarRatioMaxMACVecInclude is 20.5
No GRM will be used to fit the NULL model and nThreads is set to 1
The variance ratio file saigeqtl_custom.varianceRatio.txt already exists. IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten
100 samples have genotypes
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
[1] "HERERE2"
formula is ENSG00000273362~sex+age+gPCs_0+gPCs_1+gPCs_2+gPCs_3+gPCs_4+gPCs_5+gPCs_6+gPCs_7+gPCs_8+gPCs_9+gPCs_10+gPCs_11+gPCs_12+gPCs_13+gPCs_14+gPCs_15+gPCs_16+gPCs_17+gPCs_18+gPCs_19+X_pca_0+X_pca_1+X_pca_2+X_pca_3+X_pca_4+X_pca_5+X_pca_6+X_pca_7+X_pca_8+X_pca_9+X_pca_10+X_pca_11+X_pca_12+X_pca_13+X_pca_14
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
4756 samples have non-missing phenotypes
Duplicated sample IDs are detected in the phenotype file. Assuming repeated measurements
[1] "Test"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -6.528342
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 16.424938
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 19.182995
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 29.310970
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 6.152439
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -16.819250
X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7
3403 0.6063020 1.2734809 2.2473614 0.3540534 -0.5550918 2.0952680 0.3178053
3404 0.7432303 0.1620283 0.5048675 0.1583861 -2.6948520 3.8191340 -0.9346381
3405 -2.5988312 1.2510157 0.2394443 0.7712063 1.1940196 -1.0500985 -0.9551591
3406 -1.4863100 1.3782900 -0.5513533 0.4036562 -0.9668955 -0.8461446 -1.0795137
3407 -2.0352464 0.9066630 -0.6750964 1.0423017 1.3768464 -0.3464014 -1.2474165
3408 -0.6999029 0.9565746 0.2724564 1.2845618 0.3556666 0.5312488 -0.7374892
X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13
3403 1.19299390 -0.3284275 0.426589670 0.6119198 0.28427064 0.7080616
3404 -1.32028370 -0.9726189 -0.638872000 -0.7694190 0.05772561 -0.4210741
3405 -1.24123940 0.3774612 0.008312405 -0.7623147 -0.96537240 1.6612436
3406 -0.03547685 0.3354667 2.754576200 3.0516508 -1.66621020 -0.6766295
3407 -0.74169606 -0.3880595 0.526785900 -0.3120816 -0.66266170 1.2966800
3408 -0.51005507 -0.4451288 -0.100540295 -0.3160223 0.87705460 -0.3503297
X_pca_14 ENSG00000273362 IndexPheno IndexGeno
3403 0.02301617 0 1 1
3404 0.75282717 0 2 1
3405 -1.38166570 0 3 1
3406 -1.75681750 0 4 1
3407 -0.75858957 0 5 1
3408 -0.29377973 0 6 1
4756 observations will be used for analysis
[1] "Test3"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -6.528342
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 16.424938
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 19.182995
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 29.310970
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 6.152439
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -16.819250
X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7
3403 0.6063020 1.2734809 2.2473614 0.3540534 -0.5550918 2.0952680 0.3178053
3404 0.7432303 0.1620283 0.5048675 0.1583861 -2.6948520 3.8191340 -0.9346381
3405 -2.5988312 1.2510157 0.2394443 0.7712063 1.1940196 -1.0500985 -0.9551591
3406 -1.4863100 1.3782900 -0.5513533 0.4036562 -0.9668955 -0.8461446 -1.0795137
3407 -2.0352464 0.9066630 -0.6750964 1.0423017 1.3768464 -0.3464014 -1.2474165
3408 -0.6999029 0.9565746 0.2724564 1.2845618 0.3556666 0.5312488 -0.7374892
X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13
3403 1.19299390 -0.3284275 0.426589670 0.6119198 0.28427064 0.7080616
3404 -1.32028370 -0.9726189 -0.638872000 -0.7694190 0.05772561 -0.4210741
3405 -1.24123940 0.3774612 0.008312405 -0.7623147 -0.96537240 1.6612436
3406 -0.03547685 0.3354667 2.754576200 3.0516508 -1.66621020 -0.6766295
3407 -0.74169606 -0.3880595 0.526785900 -0.3120816 -0.66266170 1.2966800
3408 -0.51005507 -0.4451288 -0.100540295 -0.3160223 0.87705460 -0.3503297
X_pca_14 ENSG00000273362 IndexPheno IndexGeno
3403 0.02301617 0 1 1
3404 0.75282717 0 2 1
3405 -1.38166570 0 3 1
3406 -1.75681750 0 4 1
3407 -0.75858957 0 5 1
3408 -0.29377973 0 6 1
[1] "Test4"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -6.528342
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 16.424938
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 19.182995
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 29.310970
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 6.152439
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -16.819250
X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7
3403 0.6063020 1.2734809 2.2473614 0.3540534 -0.5550918 2.0952680 0.3178053
3404 0.7432303 0.1620283 0.5048675 0.1583861 -2.6948520 3.8191340 -0.9346381
3405 -2.5988312 1.2510157 0.2394443 0.7712063 1.1940196 -1.0500985 -0.9551591
3406 -1.4863100 1.3782900 -0.5513533 0.4036562 -0.9668955 -0.8461446 -1.0795137
3407 -2.0352464 0.9066630 -0.6750964 1.0423017 1.3768464 -0.3464014 -1.2474165
3408 -0.6999029 0.9565746 0.2724564 1.2845618 0.3556666 0.5312488 -0.7374892
X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13
3403 1.19299390 -0.3284275 0.426589670 0.6119198 0.28427064 0.7080616
3404 -1.32028370 -0.9726189 -0.638872000 -0.7694190 0.05772561 -0.4210741
3405 -1.24123940 0.3774612 0.008312405 -0.7623147 -0.96537240 1.6612436
3406 -0.03547685 0.3354667 2.754576200 3.0516508 -1.66621020 -0.6766295
3407 -0.74169606 -0.3880595 0.526785900 -0.3120816 -0.66266170 1.2966800
3408 -0.51005507 -0.4451288 -0.100540295 -0.3160223 0.87705460 -0.3503297
X_pca_14 ENSG00000273362 IndexPheno IndexGeno
3403 0.02301617 0 1 1
3404 0.75282717 0 2 1
3405 -1.38166570 0 3 1
3406 -1.75681750 0 4 1
3407 -0.75858957 0 5 1
3408 -0.29377973 0 6 1
qr transformation has been performed on covariates
colnames(data.new) is ENSG00000273362 minus1 sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0 X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7 X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13 X_pca_14
out.transform$Param.transform$qrr: 38 38
[1] "isCovariateOffset=TRUE, so fixed effects coefficnets won't be estimated."
[1] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806"
[6] "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_806" "OneK1K_518"
[11] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[16] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[21] "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518" "OneK1K_518"
[26] "OneK1K_518" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[31] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[36] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[41] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[46] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[51] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[56] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[61] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[66] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[71] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[76] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[81] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[86] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161"
[91] "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_161" "OneK1K_588"
[96] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[101] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[106] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[111] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[116] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[121] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_588"
[126] "OneK1K_588" "OneK1K_588" "OneK1K_588" "OneK1K_1061" "OneK1K_1061"
[131] "OneK1K_1061" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[136] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[141] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[146] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[151] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[156] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[161] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[166] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[171] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[176] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[181] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[186] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[191] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[196] "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774" "OneK1K_774"
[1] TRUE
numofV 0
[1] "HERE"
[1] "HERE1"
[1] FALSE
num_Kmat 2
ptr_gNULLGENOobj->g_minMACVarRatio 20
ptr_gNULLGENOobj->g_maxMACVarRatio -1
Markers in the Plink file with MAF < 0.01 will be removed before constructing GRM
Markers in the Plink file with missing rate > 0.15 will be removed before constructing GRM
ENSG00000273362 is a count trait
glm:
Call: glm(formula = formula.new, family = "poisson", data = data.new,
weights = varWeights, offset = covoffset)
Coefficients:
(Intercept)
-27.3
Degrees of Freedom: 4755 Total (i.e. Null); 4755 Residual
Null Deviance: 2.42e-10
Residual Deviance: 1.321e-08 AIC: 2
[1] "isStoreSigma"
[1] TRUE
Start fitting the NULL GLMM
user system elapsed
14.474 1.948 16.295
user system elapsed
14.526 1.948 16.348
[1] "Start reading genotype plink file here"
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -6.528342
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 16.424938
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 19.182995
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 29.310970
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 6.152439
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -16.819250
X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7
3403 0.6063020 1.2734809 2.2473614 0.3540534 -0.5550918 2.0952680 0.3178053
3404 0.7432303 0.1620283 0.5048675 0.1583861 -2.6948520 3.8191340 -0.9346381
3405 -2.5988312 1.2510157 0.2394443 0.7712063 1.1940196 -1.0500985 -0.9551591
3406 -1.4863100 1.3782900 -0.5513533 0.4036562 -0.9668955 -0.8461446 -1.0795137
3407 -2.0352464 0.9066630 -0.6750964 1.0423017 1.3768464 -0.3464014 -1.2474165
3408 -0.6999029 0.9565746 0.2724564 1.2845618 0.3556666 0.5312488 -0.7374892
X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13
3403 1.19299390 -0.3284275 0.426589670 0.6119198 0.28427064 0.7080616
3404 -1.32028370 -0.9726189 -0.638872000 -0.7694190 0.05772561 -0.4210741
3405 -1.24123940 0.3774612 0.008312405 -0.7623147 -0.96537240 1.6612436
3406 -0.03547685 0.3354667 2.754576200 3.0516508 -1.66621020 -0.6766295
3407 -0.74169606 -0.3880595 0.526785900 -0.3120816 -0.66266170 1.2966800
3408 -0.51005507 -0.4451288 -0.100540295 -0.3160223 0.87705460 -0.3503297
X_pca_14 ENSG00000273362 IndexPheno IndexGeno
3403 0.02301617 0 1 1
3404 0.75282717 0 2 1
3405 -1.38166570 0 3 1
3406 -1.75681750 0 4 1
3407 -0.75858957 0 5 1
3408 -0.29377973 0 6 1
[1] "length(indicatorGenoSamplesWithPheno)"
[1] 4756
[1] "Genotype reading is done"
tauInit[1] 0 0
fixtau 1 0
tauInit 1 0
inital tau is 1 0.1
[1] "tau"
[1] 1.0 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
(Intercept)
-27.30259
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
[1] "tau0_q2 a"
[1] 0.1
[1] "idxtau"
[1] 2
[1] "re$YPAPY"
[,1]
[1,] 1.039092e-18
[1] "re$Trace"
[,1]
[1,] 2.303134e-09
Variance component estimates:
[1] 1.0 0.1
Iteration 1 1 0.1 :
tau0_v1: 1 0.1
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
1.5140e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -28.30271
[1] "alpha"
[,1]
[1,] -28.30271
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -28.30271
t_end_Get_Coef - t_begin_Get_Coef
user system elapsed
0.001 0.000 0.001
check 1
fixtauVec
1
0
g_I_longl_mat.n_rows 4756
iter from getPCG1ofSigmaAndVector 0
AI
0 0
0 0
YPAPY
0
1.0391e-18
YPAPY
0
1.0391e-18
idxtau
1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update30 1
CV for trace random estimator using 30 runs is 0.0070
> 0.0025
try 40runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update40 1
CV for trace random estimator using 40 runs is 0.0055
> 0.0025
try 50runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update50 1
CV for trace random estimator using 50 runs is 0.0046
> 0.0025
try 60runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update60 1
CV for trace random estimator using 60 runs is 0.0038
> 0.0025
try 70runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update70 1
CV for trace random estimator using 70 runs is 0.0032
> 0.0025
try 80runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update80 1
CV for trace random estimator using 80 runs is 0.0028
> 0.0025
try 90runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update90 1
CV for trace random estimator using 90 runs is 0.0025
> 0.0025
try 100runs
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
dim temp_mat_update100 1
Trace
2.3031e-09
check 2
score1
-2.3031e-09
YPAPY
1.0391e-18
Trace
2.3031e-09
score
-2.3031e-09
i 0
i 1
t_end_fitglmmaiRPCG - t_begin_fitglmmaiRPCG
user system elapsed
0.026 0.003 0.029
[1] 0.000000e+00 6.773277e-09
tau: 1 0.1
tau0: 1 0.1
Final 1 0.1 :
before Sigma_iY
Yvec.n_elem 4756
iter from getPCG1ofSigmaAndVector 1
after Sigma_iY
iter from getPCG1ofSigmaAndVector 1
cov
4.1159e+08
Tau:
[1] 1.0 0.1
Fixed-effect coefficients:
[,1]
[1,] -29.30295
[1] "alpha"
[,1]
[1,] -29.30295
[1] "alpha0"
[,1]
[1,] -28.30271
[1] "y[1]"
3403
0
[1] "y[2]"
3404
0
[1] "alpha"
[,1]
[1,] -29.30295
t_end_null - t_begin, fitting the NULL model without LOCO took
user system elapsed
0.088 0.005 0.092
sex age gPCs_0 gPCs_1 gPCs_2 gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8 gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14 gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 are sample-level covariates
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
isStoreSigma is TRUE
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
user system elapsed
14.623 1.954 16.451
t_end - t_begin, fitting the NULL model took
user system elapsed
0.149 0.006 0.156
[1] 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
[25] 2 2 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[49] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3
[73] 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 3 4 4
[97] 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4 4
[121] 4 4 4 4 4 4 4 4 5 5 5 6 6 6 6 6 6 6 6 6 6 6 6 6
[145] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[169] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[193] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[217] 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6 6
[241] 6 6 6 6 6 6 7 7 7 7 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[265] 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8 8
[289] 8 8 8 8 8 8 8 8 8 8 8 8 9 9 9 9 9 9 9 9 9 9 9 9
[313] 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 9 10
[337] 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 11 11 11 11 11 11 11 11
[361] 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 11 12 12 12 12 13 13 13 13
[385] 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13 13
[409] 13 13 14 14 14 14 15 15 15 15 15 15 15 15 15 15 16 16 16 16 16 16 16 16
[433] 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 16 17
[457] 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 17 18 18 18 18 18 18 18 18
[481] 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 18 19 19 19 19 19 19
[505] 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19 19
[529] 19 19 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[553] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[577] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[601] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[625] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[649] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[673] 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
[697] 20 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 21 22 22 22 22 22
[721] 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22 22
[745] 22 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23 23
[769] 23 23 23 23 23 23 23 23 23 23 23 23 23 23 24 24 24 24 24 24 24 24 24 24
[793] 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 24 25 25 25 25 25
[817] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[841] 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25
[865] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[889] 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26 26
[913] 26 26 26 26 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[937] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[961] 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27 27
[985] 27 27 27 27 27 27 27 27 28 28 28 28 28 28 28 28
IID (Intercept) sex age gPCs_0 gPCs_1 gPCs_2
3403 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3404 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3405 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3406 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3407 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
3408 OneK1K_806 1 1 57 -0.00362118 -0.00348333 -0.00836611
gPCs_3 gPCs_4 gPCs_5 gPCs_6 gPCs_7 gPCs_8
3403 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3404 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3405 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3406 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3407 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
3408 0.00575833 0.00507995 -0.00309699 2.34355e-05 -0.000681114 -0.000661151
gPCs_9 gPCs_10 gPCs_11 gPCs_12 gPCs_13 gPCs_14
3403 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3404 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3405 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3406 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3407 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
3408 -0.00368411 -0.00758271 0.0102165 -0.011742 0.00198527 4.3811e-05
gPCs_15 gPCs_16 gPCs_17 gPCs_18 gPCs_19 X_pca_0
3403 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -6.528342
3404 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 16.424938
3405 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 19.182995
3406 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 29.310970
3407 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 6.152439
3408 0.0134991 -0.00229497 -0.0133394 -0.00263601 8.32904e-05 -16.819250
X_pca_1 X_pca_2 X_pca_3 X_pca_4 X_pca_5 X_pca_6 X_pca_7
3403 0.6063020 1.2734809 2.2473614 0.3540534 -0.5550918 2.0952680 0.3178053
3404 0.7432303 0.1620283 0.5048675 0.1583861 -2.6948520 3.8191340 -0.9346381
3405 -2.5988312 1.2510157 0.2394443 0.7712063 1.1940196 -1.0500985 -0.9551591
3406 -1.4863100 1.3782900 -0.5513533 0.4036562 -0.9668955 -0.8461446 -1.0795137
3407 -2.0352464 0.9066630 -0.6750964 1.0423017 1.3768464 -0.3464014 -1.2474165
3408 -0.6999029 0.9565746 0.2724564 1.2845618 0.3556666 0.5312488 -0.7374892
X_pca_8 X_pca_9 X_pca_10 X_pca_11 X_pca_12 X_pca_13
3403 1.19299390 -0.3284275 0.426589670 0.6119198 0.28427064 0.7080616
3404 -1.32028370 -0.9726189 -0.638872000 -0.7694190 0.05772561 -0.4210741
3405 -1.24123940 0.3774612 0.008312405 -0.7623147 -0.96537240 1.6612436
3406 -0.03547685 0.3354667 2.754576200 3.0516508 -1.66621020 -0.6766295
3407 -0.74169606 -0.3880595 0.526785900 -0.3120816 -0.66266170 1.2966800
3408 -0.51005507 -0.4451288 -0.100540295 -0.3160223 0.87705460 -0.3503297
X_pca_14 ENSG00000273362 IndexPheno IndexGeno
3403 0.02301617 0 1 1
3404 0.75282717 0 2 1
3405 -1.38166570 0 3 1
3406 -1.75681750 0 4 1
3407 -0.75858957 0 5 1
3408 -0.29377973 0 6 1
[1] "HEREHRE"
nbyte: 25
nbyte: 25
reserve: 115479
M: 4277, N: 100
setgeno mark1
setgeno mark2
3516 markers with MAF >= 0.01 and missing rate <= 0.15
time: 9.501
Start estimating variance ratios
Family: poisson
Link function: log
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[1] "mu[1:20]"
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
iter from getPCG1ofSigmaAndVector 1
length(MACvector): 3516
length(MACvector_forVarRatio): 521
Only one variance ratio will be estimated using randomly selected markers with MAC >= 20
29 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
257 22 22_16708242_C_T 0 16708242 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2505
iter from getPCG1ofSigmaAndVector 1
AC 2354
S is -7.288191e-25
var1 is 1.898684e-10
p_exact 1
var2sparseGRM Here 1.911062e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2354
var1 1.898684e-10
var2null 1.898684e-10
var2null_noXadj 2.620976e-10
98 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 0 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
732 22 22_16849519_G_T 0 16849519 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1514
iter from getPCG1ofSigmaAndVector 1
AC 3886
S is 6.462222e-25
var1 is 2.308409e-10
p_exact 1
var2sparseGRM Here 2.391416e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3886
var1 2.308409e-10
var2null 2.308409e-10
var2null_noXadj 3.757012e-10
45 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
365 22 22_16743395_C_A 0 16743395 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3226
iter from getPCG1ofSigmaAndVector 1
AC 1676
S is 2.875366e-25
var1 is 1.867757e-10
p_exact 1
var2sparseGRM Here 1.929035e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1676
var1 1.867757e-10
var2null 1.867757e-10
var2null_noXadj 2.603938e-10
156 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1141 22 22_16962373_T_A 0 16962373 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4240
S is 2.469072e-24
var1 is 2.590711e-10
p_exact 1
var2sparseGRM Here 2.61604e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4240
var1 2.590711e-10
var2null 2.590712e-10
var2null_noXadj 5.434031e-10
377 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 2 1 0 0 2 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2888 22 22_17318326_C_T 0 17318326 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3084
iter from getPCG1ofSigmaAndVector 1
AC 1856
S is 3.624469e-25
var1 is 1.618094e-10
p_exact 1
var2sparseGRM Here 1.632641e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1856
var1 1.618094e-10
var2null 1.618094e-10
var2null_noXadj 2.849612e-10
202 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1670 22 22_17087008_A_G 0 17087008 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -7.20047e-25
var1 is 1.299618e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.299618e-10
var2null 1.299618e-10
var2null_noXadj 2.211101e-10
228 th marker in geno 1
MAC: 97
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 2 1 0 1 1 2 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1820 22 22_17125423_C_CA 0 17125423 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1400
iter from getPCG1ofSigmaAndVector 1
AC 4740
S is 4.378595e-24
var1 is 3.272621e-10
p_exact 1
var2sparseGRM Here 3.362174e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4740
var1 3.272621e-10
var2null 3.272621e-10
var2null_noXadj 5.235456e-10
212 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 0 0 1 1 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1729 22 22_17106625_T_C 0 17106625 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3055
iter from getPCG1ofSigmaAndVector 1
AC 1829
S is -5.07572e-25
var1 is 1.562356e-10
p_exact 1
var2sparseGRM Here 1.590809e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1829
var1 1.562356e-10
var2null 1.562357e-10
var2null_noXadj 2.606528e-10
492 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4005 22 22_17525225_C_T 0 17525225 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2709
iter from getPCG1ofSigmaAndVector 1
AC 2224
S is -9.174011e-25
var1 is 1.564245e-10
p_exact 1
var2sparseGRM Here 1.582023e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2224
var1 1.564245e-10
var2null 1.564246e-10
var2null_noXadj 2.943512e-10
477 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3916 22 22_17511574_A_G 0 17511574 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3781
iter from getPCG1ofSigmaAndVector 1
AC 975
S is 1.110716e-26
var1 is 1.02156e-10
p_exact 1
var2sparseGRM Here 1.030177e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 975
var1 1.02156e-10
var2null 1.02156e-10
var2null_noXadj 1.458335e-10
209 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 2 0 2 2 2 2 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1717 22 22_17104551_C_T 0 17104551 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1335
iter from getPCG1ofSigmaAndVector 1
AC 4717
S is 6.598932e-25
var1 is 2.609654e-10
p_exact 1
var2sparseGRM Here 2.633613e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4717
var1 2.609654e-10
var2null 2.609654e-10
var2null_noXadj 4.943218e-10
291 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2303 22 22_17195422_G_A 0 17195422 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3568
iter from getPCG1ofSigmaAndVector 1
AC 1473
S is -4.343153e-26
var1 is 1.704016e-10
p_exact 1
var2sparseGRM Here 1.720973e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1473
var1 1.704016e-10
var2null 1.704016e-10
var2null_noXadj 3.053241e-10
81 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 1 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
614 22 22_16822493_C_T 0 16822493 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1247
iter from getPCG1ofSigmaAndVector 1
AC 4458
S is 7.068421e-24
var1 is 2.370345e-10
p_exact 1
var2sparseGRM Here 2.425598e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4458
var1 2.370345e-10
var2null 2.370345e-10
var2null_noXadj 4.299084e-10
79 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 2 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
605 22 22_16821873_G_C 0 16821873 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1830
iter from getPCG1ofSigmaAndVector 1
AC 3534
S is 2.492643e-24
var1 is 2.345404e-10
p_exact 1
var2sparseGRM Here 2.405708e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3534
var1 2.345404e-10
var2null 2.345404e-10
var2null_noXadj 4.22828e-10
509 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 2 0 2 1 2 0 1 2 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 0
CHR 22
V1 V2 V3 V4 V5 V6
4190 22 22_17564857_C_CAAAAAAAAAAA 0 17564857 C CAAAAAAAAAAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1286
iter from getPCG1ofSigmaAndVector 1
AC 4677
S is 8.062184e-24
var1 is 2.435034e-10
p_exact 1
var2sparseGRM Here 2.477298e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4677
var1 2.435034e-10
var2null 2.435034e-10
var2null_noXadj 4.717379e-10
496 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 0 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4033 22 22_17531010_A_G 0 17531010 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3323
iter from getPCG1ofSigmaAndVector 1
AC 1520
S is -3.730997e-25
var1 is 1.397949e-10
p_exact 1
var2sparseGRM Here 1.415267e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1520
var1 1.397949e-10
var2null 1.397949e-10
var2null_noXadj 2.292737e-10
362 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2803 22 22_17302684_T_C 0 17302684 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1569
iter from getPCG1ofSigmaAndVector 1
AC 4205
S is 2.708077e-24
var1 is 2.40315e-10
p_exact 1
var2sparseGRM Here 2.418579e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4205
var1 2.40315e-10
var2null 2.40315e-10
var2null_noXadj 4.742401e-10
64 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 2 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
518 22 22_16801041_G_A 0 16801041 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3855
S is 4.037207e-24
var1 is 2.163401e-10
p_exact 1
var2sparseGRM Here 2.278228e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3855
var1 2.163401e-10
var2null 2.163401e-10
var2null_noXadj 4.297568e-10
440 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3510 22 22_17441874_G_C 0 17441874 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3425
iter from getPCG1ofSigmaAndVector 1
AC 1741
S is 2.247342e-25
var1 is 2.174521e-10
p_exact 1
var2sparseGRM Here 2.191694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1741
var1 2.174521e-10
var2null 2.174522e-10
var2null_noXadj 3.624575e-10
511 th marker in geno 1
MAC: 74
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4205 22 22_17567322_A_G 0 17567322 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2205
iter from getPCG1ofSigmaAndVector 1
AC 3081
S is 2.432847e-24
var1 is 2.198999e-10
p_exact 1
var2sparseGRM Here 2.213266e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3081
var1 2.198999e-10
var2null 2.199e-10
var2null_noXadj 4.123576e-10
489 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3985 22 22_17523014_A_AGGGG 0 17523014 A AGGGG
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2758
iter from getPCG1ofSigmaAndVector 1
AC 2166
S is -7.476256e-25
var1 is 1.436406e-10
p_exact 1
var2sparseGRM Here 1.454105e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2166
var1 1.436406e-10
var2null 1.436406e-10
var2null_noXadj 2.988042e-10
216 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1738 22 22_17108677_C_T 0 17108677 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3043
iter from getPCG1ofSigmaAndVector 1
AC 1917
S is -4.472652e-25
var1 is 2.152038e-10
p_exact 1
var2sparseGRM Here 2.160168e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1917
var1 2.152038e-10
var2null 2.152038e-10
var2null_noXadj 3.165546e-10
78 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 0 1 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
600 22 22_16821568_C_G 0 16821568 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3339
iter from getPCG1ofSigmaAndVector 1
AC 1469
S is -6.235535e-25
var1 is 1.297221e-10
p_exact 1
var2sparseGRM Here 1.304024e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1469
var1 1.297221e-10
var2null 1.297221e-10
var2null_noXadj 2.104023e-10
444 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3537 22 22_17445692_G_A 0 17445692 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3425
iter from getPCG1ofSigmaAndVector 1
AC 1741
S is 2.247342e-25
var1 is 2.174521e-10
p_exact 1
var2sparseGRM Here 2.191694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1741
var1 2.174521e-10
var2null 2.174522e-10
var2null_noXadj 3.624575e-10
227 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1819 22 22_17125117_T_TA 0 17125117 T TA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2892
iter from getPCG1ofSigmaAndVector 1
AC 2205
S is 3.943547e-25
var1 is 2.727272e-10
p_exact 1
var2sparseGRM Here 2.776581e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2205
var1 2.727272e-10
var2null 2.727272e-10
var2null_noXadj 3.505875e-10
259 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 2 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2094 22 22_17170409_AAAAAAT_A 0 17170409 AAAAAAT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3226
iter from getPCG1ofSigmaAndVector 1
AC 1636
S is 3.454106e-25
var1 is 1.493699e-10
p_exact 1
var2sparseGRM Here 1.503359e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1636
var1 1.493699e-10
var2null 1.493699e-10
var2null_noXadj 2.515179e-10
40 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
334 22 22_16738360_T_A 0 16738360 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3682
iter from getPCG1ofSigmaAndVector 1
AC 1112
S is -3.837019e-26
var1 is 1.161535e-10
p_exact 1
var2sparseGRM Here 1.184382e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1112
var1 1.161535e-10
var2null 1.161535e-10
var2null_noXadj 1.74527e-10
15 th marker in geno 1
MAC: 58
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
164 22 22_16678727_G_A 0 16678727 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2435
iter from getPCG1ofSigmaAndVector 1
AC 2601
S is -9.289626e-26
var1 is 2.150681e-10
p_exact 1
var2sparseGRM Here 2.165989e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2601
var1 2.150681e-10
var2null 2.150681e-10
var2null_noXadj 3.283047e-10
211 th marker in geno 1
MAC: 94
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 2 0 1 1 1 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1725 22 22_17105724_G_C 0 17105724 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1376
iter from getPCG1ofSigmaAndVector 1
AC 4424
S is 1.376808e-24
var1 is 2.872977e-10
p_exact 1
var2sparseGRM Here 2.888314e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4424
var1 2.872977e-10
var2null 2.872977e-10
var2null_noXadj 4.653805e-10
261 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 2 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2123 22 22_17173199_C_T 0 17173199 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2662
S is -6.354306e-25
var1 is 1.86748e-10
p_exact 1
var2sparseGRM Here 1.881904e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2662
var1 1.86748e-10
var2null 1.86748e-10
var2null_noXadj 2.652914e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355
CV for variance ratio estimate using 30 markers is 0.004294349 > 0.001
try 40 markers
269 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 2 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2164 22 22_17175884_G_GT 0 17175884 G GT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2213
iter from getPCG1ofSigmaAndVector 1
AC 2662
S is -6.354306e-25
var1 is 1.86748e-10
p_exact 1
var2sparseGRM Here 1.881904e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2662
var1 1.86748e-10
var2null 1.86748e-10
var2null_noXadj 2.652914e-10
38 th marker in geno 1
MAC: 83
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 0 0 1 1 2 0 1 1
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
306 22 22_16726908_G_T 0 16726908 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1559
iter from getPCG1ofSigmaAndVector 1
AC 4228
S is -8.584826e-25
var1 is 3.588723e-10
p_exact 1
var2sparseGRM Here 3.642216e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4228
var1 3.588723e-10
var2null 3.588723e-10
var2null_noXadj 4.798574e-10
118 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
862 22 22_16878208_T_C 0 16878208 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2813
iter from getPCG1ofSigmaAndVector 1
AC 1946
S is -9.744578e-25
var1 is 1.336059e-10
p_exact 1
var2sparseGRM Here 1.345697e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1946
var1 1.336059e-10
var2null 1.336059e-10
var2null_noXadj 2.242531e-10
19 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
181 22 22_16688797_GAA_G 0 16688797 GAA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3171
iter from getPCG1ofSigmaAndVector 1
AC 1687
S is 3.853806e-25
var1 is 1.709316e-10
p_exact 1
var2sparseGRM Here 1.733181e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1687
var1 1.709316e-10
var2null 1.709316e-10
var2null_noXadj 2.434307e-10
107 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
790 22 22_16861810_T_C 0 16861810 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3670
iter from getPCG1ofSigmaAndVector 1
AC 1168
S is -1.873929e-25
var1 is 1.134918e-10
p_exact 1
var2sparseGRM Here 1.164694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1168
var1 1.134918e-10
var2null 1.134918e-10
var2null_noXadj 2.000757e-10
372 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 0 2 1 0 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 2
CHR 22
V1 V2 V3 V4 V5 V6
2861 22 22_17310674_T_C 0 17310674 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2140
iter from getPCG1ofSigmaAndVector 1
AC 3010
S is 2.408771e-24
var1 is 2.170945e-10
p_exact 1
var2sparseGRM Here 2.197472e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3010
var1 2.170945e-10
var2null 2.170945e-10
var2null_noXadj 3.566332e-10
514 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4215 22 22_17570571_G_T 0 17570571 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2191
iter from getPCG1ofSigmaAndVector 1
AC 3425
S is -2.169961e-24
var1 is 2.601305e-10
p_exact 1
var2sparseGRM Here 2.625716e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3425
var1 2.601305e-10
var2null 2.601305e-10
var2null_noXadj 5.054694e-10
67 th marker in geno 1
MAC: 62
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 2 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
539 22 22_16805822_T_A 0 16805822 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1602
iter from getPCG1ofSigmaAndVector 1
AC 3855
S is 4.037207e-24
var1 is 2.163401e-10
p_exact 1
var2sparseGRM Here 2.278228e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3855
var1 2.163401e-10
var2null 2.163401e-10
var2null_noXadj 4.297568e-10
130 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
949 22 22_16914834_C_G 0 16914834 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3624
iter from getPCG1ofSigmaAndVector 1
AC 1136
S is 1.358103e-25
var1 is 9.669638e-11
p_exact 1
var2sparseGRM Here 9.762325e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1136
var1 9.669638e-11
var2null 9.669638e-11
var2null_noXadj 1.640285e-10
248 th marker in geno 1
MAC: 55
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1975 22 22_17151727_TAAAAAA_T 0 17151727 TAAAAAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2655
iter from getPCG1ofSigmaAndVector 1
AC 2281
S is -8.819465e-25
var1 is 2.249632e-10
p_exact 1
var2sparseGRM Here 2.267008e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2281
var1 2.249632e-10
var2null 2.249632e-10
var2null_noXadj 2.964355e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943
CV for variance ratio estimate using 40 markers is 0.003344592 > 0.001
try 50 markers
263 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2136 22 22_17174211_C_T 0 17174211 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2063
iter from getPCG1ofSigmaAndVector 1
AC 2943
S is 1.421477e-24
var1 is 2.07499e-10
p_exact 1
var2sparseGRM Here 2.114684e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2943
var1 2.07499e-10
var2null 2.07499e-10
var2null_noXadj 3.102728e-10
475 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3910 22 22_17510346_C_T 0 17510346 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3421
iter from getPCG1ofSigmaAndVector 1
AC 1382
S is 2.949078e-25
var1 is 1.384662e-10
p_exact 1
var2sparseGRM Here 1.396817e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1382
var1 1.384662e-10
var2null 1.384662e-10
var2null_noXadj 2.026389e-10
125 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
917 22 22_16906964_G_A 0 16906964 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3763
iter from getPCG1ofSigmaAndVector 1
AC 997
S is -3.736045e-26
var1 is 8.861294e-11
p_exact 1
var2sparseGRM Here 8.945318e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 997
var1 8.861294e-11
var2null 8.861295e-11
var2null_noXadj 1.499259e-10
466 th marker in geno 1
MAC: 53
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 0 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3856 22 22_17499058_T_C 0 17499058 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2780
iter from getPCG1ofSigmaAndVector 1
AC 2491
S is 3.968917e-25
var1 is 2.252102e-10
p_exact 1
var2sparseGRM Here 2.26651e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2491
var1 2.252102e-10
var2null 2.252102e-10
var2null_noXadj 4.164441e-10
8 th marker in geno 1
MAC: 43
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 0 0 0 0 2
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
110 22 22_16594856_C_CT 0 16594856 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3119
iter from getPCG1ofSigmaAndVector 1
AC 1699
S is -9.689231e-25
var1 is 1.452277e-10
p_exact 1
var2sparseGRM Here 1.463612e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1699
var1 1.452277e-10
var2null 1.452277e-10
var2null_noXadj 2.332095e-10
244 th marker in geno 1
MAC: 47
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 2 1 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1952 22 22_17147758_C_T 0 17147758 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2693
iter from getPCG1ofSigmaAndVector 1
AC 2355
S is 1.717319e-25
var1 is 2.706395e-10
p_exact 1
var2sparseGRM Here 2.721232e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2355
var1 2.706395e-10
var2null 2.706395e-10
var2null_noXadj 3.333022e-10
223 th marker in geno 1
MAC: 57
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1787 22 22_17117420_C_T 0 17117420 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2867
iter from getPCG1ofSigmaAndVector 1
AC 2268
S is -8.719122e-26
var1 is 2.341592e-10
p_exact 1
var2sparseGRM Here 2.357622e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2268
var1 2.341592e-10
var2null 2.341593e-10
var2null_noXadj 3.730813e-10
95 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
704 22 22_16842702_G_A 0 16842702 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3850
iter from getPCG1ofSigmaAndVector 1
AC 988
S is -1.309067e-25
var1 is 1.270925e-10
p_exact 1
var2sparseGRM Here 1.296929e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 988
var1 1.270925e-10
var2null 1.270925e-10
var2null_noXadj 1.985963e-10
198 th marker in geno 1
MAC: 96
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 0 1 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1627 22 22_17074025_G_A 0 17074025 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1584
iter from getPCG1ofSigmaAndVector 1
AC 4675
S is 3.830835e-25
var1 is 3.467246e-10
p_exact 1
var2sparseGRM Here 3.515688e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4675
var1 3.467246e-10
var2null 3.467246e-10
var2null_noXadj 5.802089e-10
180 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 0 0 2 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1517 22 22_17046605_G_C 0 17046605 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1628
iter from getPCG1ofSigmaAndVector 1
AC 4631
S is 4.494361e-25
var1 is 3.455957e-10
p_exact 1
var2sparseGRM Here 3.501664e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4631
var1 3.455957e-10
var2null 3.455957e-10
var2null_noXadj 5.893541e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973
CV for variance ratio estimate using 50 markers is 0.002611147 > 0.001
try 60 markers
415 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3261 22 22_17408995_A_T 0 17408995 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 909
iter from getPCG1ofSigmaAndVector 1
AC 4494
S is 5.996176e-24
var1 is 2.129055e-10
p_exact 1
var2sparseGRM Here 2.173729e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4494
var1 2.129055e-10
var2null 2.129055e-10
var2null_noXadj 2.896567e-10
258 th marker in geno 1
MAC: 44
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 2 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2090 22 22_17170041_C_T 0 17170041 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3226
iter from getPCG1ofSigmaAndVector 1
AC 1636
S is 3.454106e-25
var1 is 1.493699e-10
p_exact 1
var2sparseGRM Here 1.503359e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1636
var1 1.493699e-10
var2null 1.493699e-10
var2null_noXadj 2.515179e-10
189 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1556 22 22_17054364_T_C 0 17054364 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -7.20047e-25
var1 is 1.299618e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.299618e-10
var2null 1.299618e-10
var2null_noXadj 2.211101e-10
31 th marker in geno 1
MAC: 61
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 1 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
269 22 22_16713436_T_C 0 16713436 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1683
iter from getPCG1ofSigmaAndVector 1
AC 3623
S is 2.575139e-24
var1 is 2.132199e-10
p_exact 1
var2sparseGRM Here 2.155607e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3623
var1 2.132199e-10
var2null 2.132199e-10
var2null_noXadj 3.867934e-10
105 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 1 0 0 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
774 22 22_16859187_A_G 0 16859187 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2531
iter from getPCG1ofSigmaAndVector 1
AC 2634
S is -3.986714e-25
var1 is 2.006466e-10
p_exact 1
var2sparseGRM Here 2.110578e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2634
var1 2.006466e-10
var2null 2.006466e-10
var2null_noXadj 3.8236e-10
284 th marker in geno 1
MAC: 36
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2265 22 22_17187678_A_G 0 17187678 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2654
iter from getPCG1ofSigmaAndVector 1
AC 2187
S is 1.399755e-25
var1 is 1.525309e-10
p_exact 1
var2sparseGRM Here 1.550969e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2187
var1 1.525309e-10
var2null 1.525309e-10
var2null_noXadj 2.611049e-10
383 th marker in geno 1
MAC: 25
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 1 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2917 22 22_17323505_T_C 0 17323505 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3960
iter from getPCG1ofSigmaAndVector 1
AC 851
S is 1.774543e-25
var1 is 9.341746e-11
p_exact 1
var2sparseGRM Here 9.384954e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 851
var1 9.341746e-11
var2null 9.341748e-11
var2null_noXadj 1.578195e-10
136 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 2 2 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
975 22 22_16924021_C_G 0 16924021 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1636
iter from getPCG1ofSigmaAndVector 1
AC 3709
S is 1.00853e-24
var1 is 3.095815e-10
p_exact 1
var2sparseGRM Here 3.128196e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3709
var1 3.095815e-10
var2null 3.095815e-10
var2null_noXadj 3.804751e-10
190 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1565 22 22_17055665_A_G 0 17055665 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -7.20047e-25
var1 is 1.299618e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.299618e-10
var2null 1.299618e-10
var2null_noXadj 2.211101e-10
264 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 2 0 0 0 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2137 22 22_17174286_G_C 0 17174286 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1387
iter from getPCG1ofSigmaAndVector 1
AC 3675
S is 3.447259e-24
var1 is 1.695547e-10
p_exact 1
var2sparseGRM Here 1.708824e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3675
var1 1.695547e-10
var2null 1.695547e-10
var2null_noXadj 2.7193e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232
CV for variance ratio estimate using 60 markers is 0.002188348 > 0.001
try 70 markers
39 th marker in geno 1
MAC: 21
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
323 22 22_16733220_A_G 0 16733220 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3682
iter from getPCG1ofSigmaAndVector 1
AC 1112
S is -3.837019e-26
var1 is 1.161535e-10
p_exact 1
var2sparseGRM Here 1.184382e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1112
var1 1.161535e-10
var2null 1.161535e-10
var2null_noXadj 1.74527e-10
310 th marker in geno 1
MAC: 95
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 2 2 1 1 0 2 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
2445 22 22_17216771_A_C 0 17216771 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1431
iter from getPCG1ofSigmaAndVector 1
AC 4021
S is 1.817106e-24
var1 is 2.108843e-10
p_exact 1
var2sparseGRM Here 2.127067e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4021
var1 2.108843e-10
var2null 2.108844e-10
var2null_noXadj 4.121057e-10
304 th marker in geno 1
MAC: 91
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 1 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2412 22 22_17211494_G_A 0 17211494 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1200
iter from getPCG1ofSigmaAndVector 1
AC 4730
S is 4.84247e-25
var1 is 2.630588e-10
p_exact 1
var2sparseGRM Here 2.677359e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4730
var1 2.630588e-10
var2null 2.630589e-10
var2null_noXadj 4.525362e-10
252 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2029 22 22_17160649_GA_G 0 17160649 GA G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2948
iter from getPCG1ofSigmaAndVector 1
AC 1980
S is -9.464942e-25
var1 is 2.135813e-10
p_exact 1
var2sparseGRM Here 2.152827e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1980
var1 2.135813e-10
var2null 2.135813e-10
var2null_noXadj 2.900574e-10
397 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 1 2 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3059 22 22_17358468_C_T 0 17358468 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1408
iter from getPCG1ofSigmaAndVector 1
AC 4324
S is 4.831199e-24
var1 is 3.33504e-10
p_exact 1
var2sparseGRM Here 3.352441e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4324
var1 3.33504e-10
var2null 3.33504e-10
var2null_noXadj 4.405426e-10
393 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3045 22 22_17353687_T_C 0 17353687 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1358
iter from getPCG1ofSigmaAndVector 1
AC 4615
S is 5.537273e-24
var1 is 3.113248e-10
p_exact 1
var2sparseGRM Here 3.143912e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4615
var1 3.113248e-10
var2null 3.113249e-10
var2null_noXadj 4.918876e-10
428 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
3392 22 22_17427809_A_G 0 17427809 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3988
iter from getPCG1ofSigmaAndVector 1
AC 768
S is 4.44034e-26
var1 is 8.755556e-11
p_exact 1
var2sparseGRM Here 8.795466e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 768
var1 8.755556e-11
var2null 8.755557e-11
var2null_noXadj 1.251892e-10
417 th marker in geno 1
MAC: 88
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 1 1 1 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3298 22 22_17417019_CT_C 0 17417019 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1232
iter from getPCG1ofSigmaAndVector 1
AC 4229
S is 3.032078e-24
var1 is 2.476816e-10
p_exact 1
var2sparseGRM Here 2.500833e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4229
var1 2.476816e-10
var2null 2.476816e-10
var2null_noXadj 3.529596e-10
36 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
299 22 22_16724286_T_C 0 16724286 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3626
iter from getPCG1ofSigmaAndVector 1
AC 1168
S is -6.594877e-26
var1 is 1.191615e-10
p_exact 1
var2sparseGRM Here 1.211955e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1168
var1 1.191615e-10
var2null 1.191615e-10
var2null_noXadj 1.79862e-10
155 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1122 22 22_16958936_G_A 0 16958936 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4240
S is 2.469072e-24
var1 is 2.590711e-10
p_exact 1
var2sparseGRM Here 2.61604e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4240
var1 2.590711e-10
var2null 2.590712e-10
var2null_noXadj 5.434031e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
CV for variance ratio estimate using 70 markers is 0.001904197 > 0.001
try 80 markers
162 th marker in geno 1
MAC: 76
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 2 0 1 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
1201 22 22_16975883_A_C 0 16975883 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1697
iter from getPCG1ofSigmaAndVector 1
AC 4240
S is 2.469072e-24
var1 is 2.590711e-10
p_exact 1
var2sparseGRM Here 2.61604e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4240
var1 2.590711e-10
var2null 2.590712e-10
var2null_noXadj 5.434031e-10
293 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2318 22 22_17196323_C_CA 0 17196323 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2570
iter from getPCG1ofSigmaAndVector 1
AC 2601
S is 1.701415e-26
var1 is 2.612498e-10
p_exact 1
var2sparseGRM Here 2.626044e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2601
var1 2.612498e-10
var2null 2.612498e-10
var2null_noXadj 3.785884e-10
27 th marker in geno 1
MAC: 60
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 1 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
246 22 22_16705760_TA_T 0 16705760 TA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1725
iter from getPCG1ofSigmaAndVector 1
AC 3581
S is 2.79279e-24
var1 is 2.283352e-10
p_exact 1
var2sparseGRM Here 2.300741e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3581
var1 2.283352e-10
var2null 2.283352e-10
var2null_noXadj 3.911526e-10
58 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
477 22 22_16788186_C_T 0 16788186 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2719
iter from getPCG1ofSigmaAndVector 1
AC 2037
S is -6.13393e-25
var1 is 1.345854e-10
p_exact 1
var2sparseGRM Here 1.381819e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2037
var1 1.345854e-10
var2null 1.345855e-10
var2null_noXadj 2.274347e-10
48 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 1 1 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
384 22 22_16747765_CT_C 0 16747765 CT C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2030
iter from getPCG1ofSigmaAndVector 1
AC 3386
S is -2.328301e-24
var1 is 2.714608e-10
p_exact 1
var2sparseGRM Here 2.792879e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3386
var1 2.714608e-10
var2null 2.714608e-10
var2null_noXadj 4.518904e-10
127 th marker in geno 1
MAC: 22
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
930 22 22_16908129_T_A 0 16908129 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3763
iter from getPCG1ofSigmaAndVector 1
AC 997
S is -3.736045e-26
var1 is 8.861294e-11
p_exact 1
var2sparseGRM Here 8.945318e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 997
var1 8.861294e-11
var2null 8.861295e-11
var2null_noXadj 1.499259e-10
367 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2842 22 22_17307364_G_A 0 17307364 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2134
iter from getPCG1ofSigmaAndVector 1
AC 3295
S is -1.927951e-24
var1 is 2.246564e-10
p_exact 1
var2sparseGRM Here 2.265091e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3295
var1 2.246564e-10
var2null 2.246564e-10
var2null_noXadj 4.431122e-10
123 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
886 22 22_16886615_AT_A 0 16886615 AT A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3877
iter from getPCG1ofSigmaAndVector 1
AC 955
S is 3.395257e-26
var1 is 1.030316e-10
p_exact 1
var2sparseGRM Here 1.049041e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 955
var1 1.030316e-10
var2null 1.030316e-10
var2null_noXadj 1.720337e-10
94 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 1 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
686 22 22_16839591_T_C 0 16839591 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3928
iter from getPCG1ofSigmaAndVector 1
AC 910
S is -1.178874e-26
var1 is 1.200331e-10
p_exact 1
var2sparseGRM Here 1.222802e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 910
var1 1.200331e-10
var2null 1.200331e-10
var2null_noXadj 1.816556e-10
279 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2242 22 22_17184523_T_C 0 17184523 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3571
iter from getPCG1ofSigmaAndVector 1
AC 1297
S is -1.635782e-25
var1 is 9.890445e-11
p_exact 1
var2sparseGRM Here 9.989264e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1297
var1 9.890445e-11
var2null 9.890446e-11
var2null_noXadj 2.193226e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542
CV for variance ratio estimate using 80 markers is 0.001681503 > 0.001
try 90 markers
236 th marker in geno 1
MAC: 45
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 1 1 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1864 22 22_17131854_G_A 0 17131854 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2673
iter from getPCG1ofSigmaAndVector 1
AC 2610
S is -5.754772e-25
var1 is 2.376155e-10
p_exact 1
var2sparseGRM Here 2.390787e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2610
var1 2.376155e-10
var2null 2.376155e-10
var2null_noXadj 4.263398e-10
450 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3566 22 22_17448910_C_T 0 17448910 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3425
iter from getPCG1ofSigmaAndVector 1
AC 1741
S is 2.247342e-25
var1 is 2.174521e-10
p_exact 1
var2sparseGRM Here 2.191694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1741
var1 2.174521e-10
var2null 2.174522e-10
var2null_noXadj 3.624575e-10
166 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1369 22 22_17014255_C_T 0 17014255 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3439
iter from getPCG1ofSigmaAndVector 1
AC 1365
S is 2.031853e-25
var1 is 1.419522e-10
p_exact 1
var2sparseGRM Here 1.440446e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1365
var1 1.419522e-10
var2null 1.419522e-10
var2null_noXadj 2.013646e-10
413 th marker in geno 1
MAC: 93
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 2 1 2 1 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
3251 22 22_17406562_G_A 0 17406562 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 909
iter from getPCG1ofSigmaAndVector 1
AC 4494
S is 5.996176e-24
var1 is 2.129055e-10
p_exact 1
var2sparseGRM Here 2.173729e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4494
var1 2.129055e-10
var2null 2.129055e-10
var2null_noXadj 2.896567e-10
68 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 0 0 1 0 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
543 22 22_16806309_C_CAT 0 16806309 C CAT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3557
iter from getPCG1ofSigmaAndVector 1
AC 1211
S is -1.911568e-26
var1 is 1.13045e-10
p_exact 1
var2sparseGRM Here 1.163936e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1211
var1 1.13045e-10
var2null 1.13045e-10
var2null_noXadj 1.743132e-10
276 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 1 0 1 1 1 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2207 22 22_17179611_C_G 0 17179611 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 980
iter from getPCG1ofSigmaAndVector 1
AC 4237
S is 1.226609e-24
var1 is 1.891769e-10
p_exact 1
var2sparseGRM Here 1.916048e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4237
var1 1.891769e-10
var2null 1.891769e-10
var2null_noXadj 2.659439e-10
25 th marker in geno 1
MAC: 86
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 0 0 0 0 0 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
226 22 22_16697442_G_T 0 16697442 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 995
iter from getPCG1ofSigmaAndVector 1
AC 4722
S is 7.140832e-24
var1 is 2.376063e-10
p_exact 1
var2sparseGRM Here 2.4055e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4722
var1 2.376063e-10
var2null 2.376063e-10
var2null_noXadj 3.868031e-10
182 th marker in geno 1
MAC: 34
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1525 22 22_17049480_A_G 0 17049480 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3708
iter from getPCG1ofSigmaAndVector 1
AC 1083
S is 2.45645e-25
var1 is 9.612722e-11
p_exact 1
var2sparseGRM Here 9.715822e-11
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1083
var1 9.612722e-11
var2null 9.612724e-11
var2null_noXadj 1.81562e-10
175 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 0 0 0 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1479 22 22_17037865_G_T 0 17037865 G T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3246
iter from getPCG1ofSigmaAndVector 1
AC 1567
S is -7.20047e-25
var1 is 1.299618e-10
p_exact 1
var2sparseGRM Here 1.303818e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1567
var1 1.299618e-10
var2null 1.299618e-10
var2null_noXadj 2.211101e-10
85 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
629 22 22_16825380_G_A 0 16825380 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2051
iter from getPCG1ofSigmaAndVector 1
AC 3270
S is 1.246703e-24
var1 is 2.374659e-10
p_exact 1
var2sparseGRM Here 2.391828e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3270
var1 2.374659e-10
var2null 2.374659e-10
var2null_noXadj 4.199451e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 1.0000000 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542 0.5573382 0.5999383 0.7049514 0.7350271
[85] 0.6485165 0.7113415 0.6142823 0.5294457 0.5877695 0.5654688
CV for variance ratio estimate using 90 markers is 0.001465559 > 0.001
try 100 markers
57 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
470 22 22_16785735_A_C 0 16785735 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -7.276958e-25
var1 is 1.346388e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.346388e-10
var2null 1.346388e-10
var2null_noXadj 2.290779e-10
86 th marker in geno 1
MAC: 90
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 1 0 0 1 1 2 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
630 22 22_16826051_T_TAAC 0 16826051 T TAAC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1247
iter from getPCG1ofSigmaAndVector 1
AC 4562
S is 6.170483e-24
var1 is 2.502709e-10
p_exact 1
var2sparseGRM Here 2.573882e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4562
var1 2.502709e-10
var2null 2.502709e-10
var2null_noXadj 4.509634e-10
482 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3961 22 22_17519297_T_G 0 17519297 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2709
iter from getPCG1ofSigmaAndVector 1
AC 2224
S is -9.174011e-25
var1 is 1.564245e-10
p_exact 1
var2sparseGRM Here 1.582023e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2224
var1 1.564245e-10
var2null 1.564246e-10
var2null_noXadj 2.943512e-10
205 th marker in geno 1
MAC: 20
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1706 22 22_17100141_TAA_T 0 17100141 TAA T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3791
iter from getPCG1ofSigmaAndVector 1
AC 965
S is 2.057728e-25
var1 is 9.526261e-11
p_exact 1
var2sparseGRM Here 1.004132e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 965
var1 9.526261e-11
var2null 9.526262e-11
var2null_noXadj 1.445651e-10
240 th marker in geno 1
MAC: 65
[1] "length(G0) aaaaa"
[1] 100
G0 2 1 2 2 1 0 0 1 0 0
[1] 4756 100
[1] 100
G0 2 2 2 2 2 2 2 2 2 1
CHR 22
V1 V2 V3 V4 V5 V6
1915 22 22_17137274_C_G 0 17137274 C G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2388
iter from getPCG1ofSigmaAndVector 1
AC 2606
S is 2.387282e-25
var1 is 2.053662e-10
p_exact 1
var2sparseGRM Here 2.084404e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2606
var1 2.053662e-10
var2null 2.053663e-10
var2null_noXadj 3.219937e-10
148 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 2 0 0 0 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1078 22 22_16947190_T_C 0 16947190 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1816
iter from getPCG1ofSigmaAndVector 1
AC 3711
S is -5.106265e-25
var1 is 2.541569e-10
p_exact 1
var2sparseGRM Here 2.565105e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3711
var1 2.541569e-10
var2null 2.541569e-10
var2null_noXadj 4.580809e-10
484 th marker in geno 1
MAC: 38
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3973 22 22_17521351_T_A 0 17521351 T A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2709
iter from getPCG1ofSigmaAndVector 1
AC 2224
S is -9.174011e-25
var1 is 1.564245e-10
p_exact 1
var2sparseGRM Here 1.582023e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2224
var1 1.564245e-10
var2null 1.564246e-10
var2null_noXadj 2.943512e-10
141 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 2 1 0 2 0 0 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1005 22 22_16931326_A_G 0 16931326 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2194
iter from getPCG1ofSigmaAndVector 1
AC 2914
S is -6.616839e-25
var1 is 2.589683e-10
p_exact 1
var2sparseGRM Here 2.612363e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2914
var1 2.589683e-10
var2null 2.589683e-10
var2null_noXadj 3.455574e-10
56 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
457 22 22_16781299_C_T 0 16781299 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -7.276958e-25
var1 is 1.346388e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.346388e-10
var2null 1.346388e-10
var2null_noXadj 2.290779e-10
363 th marker in geno 1
MAC: 89
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 1 2 1 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2808 22 22_17303033_G_A 0 17303033 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1531
iter from getPCG1ofSigmaAndVector 1
AC 4283
S is 3.385387e-24
var1 is 2.534798e-10
p_exact 1
var2sparseGRM Here 2.551599e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4283
var1 2.534798e-10
var2null 2.534798e-10
var2null_noXadj 4.775926e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 1.0000000 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 0.9999999 1.0000000 0.9999999 1.0000000
[99] 1.0000000 0.9999999
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542 0.5573382 0.5999383 0.7049514 0.7350271
[85] 0.6485165 0.7113415 0.6142823 0.5294457 0.5877695 0.5654688 0.5877424
[92] 0.5549693 0.5314215 0.6589600 0.6377957 0.5548297 0.5314215 0.7494220
[99] 0.5877424 0.5307448
CV for variance ratio estimate using 100 markers is 0.001307151 > 0.001
try 110 markers
91 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
671 22 22_16836343_A_C 0 16836343 A C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3691
iter from getPCG1ofSigmaAndVector 1
AC 1335
S is 1.540172e-25
var1 is 2.001295e-10
p_exact 1
var2sparseGRM Here 2.07046e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1335
var1 2.001295e-10
var2null 2.001296e-10
var2null_noXadj 2.94594e-10
344 th marker in geno 1
MAC: 29
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 1 1 0 0 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2642 22 22_17250567_T_TAAAATAA 0 17250567 T TAAAATAA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3527
iter from getPCG1ofSigmaAndVector 1
AC 1259
S is 1.410736e-25
var1 is 1.182098e-10
p_exact 1
var2sparseGRM Here 1.194952e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1259
var1 1.182098e-10
var2null 1.182098e-10
var2null_noXadj 1.863129e-10
253 th marker in geno 1
MAC: 48
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 1 0 0 0 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2036 22 22_17161022_A_G 0 17161022 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2780
iter from getPCG1ofSigmaAndVector 1
AC 2540
S is -1.621854e-24
var1 is 3.019687e-10
p_exact 1
var2sparseGRM Here 3.050987e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2540
var1 3.019687e-10
var2null 3.019687e-10
var2null_noXadj 4.360244e-10
322 th marker in geno 1
MAC: 37
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 1 1 0 0 1 1 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2485 22 22_17221690_T_C 0 17221690 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2825
iter from getPCG1ofSigmaAndVector 1
AC 2776
S is -7.184819e-25
var1 is 2.628984e-10
p_exact 1
var2sparseGRM Here 2.652915e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2776
var1 2.628984e-10
var2null 2.628984e-10
var2null_noXadj 5.71731e-10
438 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3507 22 22_17441603_A_AC 0 17441603 A AC
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3425
iter from getPCG1ofSigmaAndVector 1
AC 1741
S is 2.247342e-25
var1 is 2.174521e-10
p_exact 1
var2sparseGRM Here 2.191694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1741
var1 2.174521e-10
var2null 2.174522e-10
var2null_noXadj 3.624575e-10
518 th marker in geno 1
MAC: 77
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 2 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
4231 22 22_17572793_C_T 0 17572793 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2192
iter from getPCG1ofSigmaAndVector 1
AC 3456
S is -2.422598e-24
var1 is 2.672987e-10
p_exact 1
var2sparseGRM Here 2.696096e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3456
var1 2.672987e-10
var2null 2.672987e-10
var2null_noXadj 5.152126e-10
52 th marker in geno 1
MAC: 51
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 1 0 1 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
449 22 22_16769333_T_C 0 16769333 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2221
iter from getPCG1ofSigmaAndVector 1
AC 2799
S is 1.194272e-24
var1 is 2.095501e-10
p_exact 1
var2sparseGRM Here 2.164418e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2799
var1 2.095501e-10
var2null 2.095501e-10
var2null_noXadj 3.211035e-10
195 th marker in geno 1
MAC: 35
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 2 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
1607 22 22_17066270_C_A 0 17066270 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2986
iter from getPCG1ofSigmaAndVector 1
AC 2053
S is -4.750836e-25
var1 is 1.907702e-10
p_exact 1
var2sparseGRM Here 1.943832e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2053
var1 1.907702e-10
var2null 1.907702e-10
var2null_noXadj 3.301524e-10
504 th marker in geno 1
MAC: 82
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 0 0 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
4156 22 22_17556556_G_A 0 17556556 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1761
iter from getPCG1ofSigmaAndVector 1
AC 3979
S is 2.406845e-24
var1 is 2.658303e-10
p_exact 1
var2sparseGRM Here 2.678258e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3979
var1 2.658303e-10
var2null 2.658304e-10
var2null_noXadj 4.92524e-10
204 th marker in geno 1
MAC: 100
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 0 1 2 1 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1685 22 22_17092382_A_G 0 17092382 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1299
iter from getPCG1ofSigmaAndVector 1
AC 4534
S is 4.960048e-24
var1 is 2.135156e-10
p_exact 1
var2sparseGRM Here 2.151408e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4534
var1 2.135156e-10
var2null 2.135156e-10
var2null_noXadj 4.47335e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 1.0000000 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 0.9999999 1.0000000 0.9999999 1.0000000
[99] 1.0000000 0.9999999 0.9999999 0.9999999 1.0000000 0.9999999 1.0000000
[106] 0.9999998 1.0000000 0.9999999 0.9999998 0.9999999
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542 0.5573382 0.5999383 0.7049514 0.7350271
[85] 0.6485165 0.7113415 0.6142823 0.5294457 0.5877695 0.5654688 0.5877424
[92] 0.5549693 0.5314215 0.6589600 0.6377957 0.5548297 0.5314215 0.7494220
[99] 0.5877424 0.5307448 0.6793402 0.6344690 0.6925500 0.4598288 0.5999383
[106] 0.5188123 0.6525936 0.5778247 0.5397307 0.4773059
CV for variance ratio estimate using 110 markers is 0.00119768 > 0.001
try 120 markers
515 th marker in geno 1
MAC: 50
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 0 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
4216 22 22_17570663_A_G 0 17570663 A G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2496
iter from getPCG1ofSigmaAndVector 1
AC 2660
S is 8.508591e-25
var1 is 1.696682e-10
p_exact 1
var2sparseGRM Here 1.741264e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2660
var1 1.696682e-10
var2null 1.696682e-10
var2null_noXadj 3.727302e-10
44 th marker in geno 1
MAC: 30
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
362 22 22_16743136_G_A 0 16743136 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3226
iter from getPCG1ofSigmaAndVector 1
AC 1676
S is 2.875366e-25
var1 is 1.867757e-10
p_exact 1
var2sparseGRM Here 1.929035e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1676
var1 1.867757e-10
var2null 1.867757e-10
var2null_noXadj 2.603938e-10
286 th marker in geno 1
MAC: 64
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 2 1 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2276 22 22_17188516_G_C 0 17188516 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2273
iter from getPCG1ofSigmaAndVector 1
AC 3373
S is 3.079208e-25
var1 is 2.787202e-10
p_exact 1
var2sparseGRM Here 2.827462e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3373
var1 2.787202e-10
var2null 2.787202e-10
var2null_noXadj 5.229961e-10
213 th marker in geno 1
MAC: 63
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 2 0 0 0 0 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
1732 22 22_17106856_GGGC_G 0 17106856 GGGC G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2932
iter from getPCG1ofSigmaAndVector 1
AC 2045
S is -2.976593e-25
var1 is 2.162227e-10
p_exact 1
var2sparseGRM Here 2.172737e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2045
var1 2.162227e-10
var2null 2.162227e-10
var2null_noXadj 3.378065e-10
93 th marker in geno 1
MAC: 85
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 0 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
681 22 22_16839471_A_T 0 16839471 A T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1500
iter from getPCG1ofSigmaAndVector 1
AC 3900
S is 6.249924e-25
var1 is 2.294961e-10
p_exact 1
var2sparseGRM Here 2.376669e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3900
var1 2.294961e-10
var2null 2.294962e-10
var2null_noXadj 3.742329e-10
59 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 1 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
481 22 22_16790535_G_A 0 16790535 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2722
iter from getPCG1ofSigmaAndVector 1
AC 2034
S is -7.276958e-25
var1 is 1.346388e-10
p_exact 1
var2sparseGRM Here 1.382511e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2034
var1 1.346388e-10
var2null 1.346388e-10
var2null_noXadj 2.290779e-10
256 th marker in geno 1
MAC: 41
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
2062 22 22_17166972_T_G 0 17166972 T G
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3121
iter from getPCG1ofSigmaAndVector 1
AC 2121
S is 1.406381e-25
var1 is 2.57869e-10
p_exact 1
var2sparseGRM Here 2.604264e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2121
var1 2.57869e-10
var2null 2.57869e-10
var2null_noXadj 4.040096e-10
346 th marker in geno 1
MAC: 33
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 0 1 0 0 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2657 22 22_17251532_C_CA 0 17251532 C CA
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3312
iter from getPCG1ofSigmaAndVector 1
AC 1510
S is -2.376428e-25
var1 is 1.455526e-10
p_exact 1
var2sparseGRM Here 1.464983e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1510
var1 1.455526e-10
var2null 1.455527e-10
var2null_noXadj 2.188832e-10
335 th marker in geno 1
MAC: 66
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 0 1 1 1 2 0 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
2588 22 22_17243159_C_A 0 17243159 C A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2342
iter from getPCG1ofSigmaAndVector 1
AC 2794
S is -1.199321e-24
var1 is 2.208876e-10
p_exact 1
var2sparseGRM Here 2.263955e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2794
var1 2.208876e-10
var2null 2.208877e-10
var2null_noXadj 3.654352e-10
109 th marker in geno 1
MAC: 31
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 0 0 0 1 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
801 22 22_16864232_G_A 0 16864232 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3687
iter from getPCG1ofSigmaAndVector 1
AC 1151
S is -1.629006e-25
var1 is 1.113399e-10
p_exact 1
var2sparseGRM Here 1.143525e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1151
var1 1.113399e-10
var2null 1.113399e-10
var2null_noXadj 1.977362e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 1.0000000 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 0.9999999 1.0000000 0.9999999 1.0000000
[99] 1.0000000 0.9999999 0.9999999 0.9999999 1.0000000 0.9999999 1.0000000
[106] 0.9999998 1.0000000 0.9999999 0.9999998 0.9999999 1.0000000 1.0000000
[113] 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 0.9999998 1.0000000
[120] 0.9999999
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542 0.5573382 0.5999383 0.7049514 0.7350271
[85] 0.6485165 0.7113415 0.6142823 0.5294457 0.5877695 0.5654688 0.5877424
[92] 0.5549693 0.5314215 0.6589600 0.6377957 0.5548297 0.5314215 0.7494220
[99] 0.5877424 0.5307448 0.6793402 0.6344690 0.6925500 0.4598288 0.5999383
[106] 0.5188123 0.6525936 0.5778247 0.5397307 0.4773059 0.4552038 0.7172815
[113] 0.5329297 0.6400785 0.6132442 0.5877424 0.6382745 0.6649785 0.6044509
[120] 0.5630728
CV for variance ratio estimate using 120 markers is 0.001087712 > 0.001
try 130 markers
442 th marker in geno 1
MAC: 39
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 1 1 2 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
3521 22 22_17443691_C_T 0 17443691 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3425
iter from getPCG1ofSigmaAndVector 1
AC 1741
S is 2.247342e-25
var1 is 2.174521e-10
p_exact 1
var2sparseGRM Here 2.191694e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1741
var1 2.174521e-10
var2null 2.174522e-10
var2null_noXadj 3.624575e-10
203 th marker in geno 1
MAC: 69
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 1 0 1 2 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
1679 22 22_17090465_G_A 0 17090465 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2199
iter from getPCG1ofSigmaAndVector 1
AC 3353
S is -2.252356e-24
var1 is 3.233625e-10
p_exact 1
var2sparseGRM Here 3.292601e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3353
var1 3.233625e-10
var2null 3.233625e-10
var2null_noXadj 4.851515e-10
392 th marker in geno 1
MAC: 92
[1] "length(G0) aaaaa"
[1] 100
G0 1 1 1 2 1 1 2 1 1 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 1
CHR 22
V1 V2 V3 V4 V5 V6
3032 22 22_17352210_T_C 0 17352210 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1358
iter from getPCG1ofSigmaAndVector 1
AC 4615
S is 5.537273e-24
var1 is 3.113248e-10
p_exact 1
var2sparseGRM Here 3.143912e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 4615
var1 3.113248e-10
var2null 3.113249e-10
var2null_noXadj 4.918876e-10
294 th marker in geno 1
MAC: 98
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 2 1 2 2 1 2 1 2
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
2319 22 22_17196809_C_T 0 17196809 C T
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1689
iter from getPCG1ofSigmaAndVector 1
AC 3849
S is 1.217421e-24
var1 is 2.325055e-10
p_exact 1
var2sparseGRM Here 2.341887e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3849
var1 2.325055e-10
var2null 2.325056e-10
var2null_noXadj 4.5484e-10
154 th marker in geno 1
MAC: 56
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 1 0 0 0 0 1 1 1
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1100 22 22_16954034_G_C 0 16954034 G C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2218
iter from getPCG1ofSigmaAndVector 1
AC 2784
S is 4.015618e-25
var1 is 1.717806e-10
p_exact 1
var2sparseGRM Here 1.733238e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 2784
var1 1.717806e-10
var2null 1.717807e-10
var2null_noXadj 3.098955e-10
80 th marker in geno 1
MAC: 81
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 1 1 1 1 1 0 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
612 22 22_16822150_T_C 0 16822150 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 2051
iter from getPCG1ofSigmaAndVector 1
AC 3270
S is 1.246703e-24
var1 is 2.374659e-10
p_exact 1
var2sparseGRM Here 2.391828e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3270
var1 2.374659e-10
var2null 2.374659e-10
var2null_noXadj 4.199451e-10
243 th marker in geno 1
MAC: 32
[1] "length(G0) aaaaa"
[1] 100
G0 0 1 0 0 0 1 1 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 1
CHR 22
V1 V2 V3 V4 V5 V6
1948 22 22_17145775_T_C 0 17145775 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3327
iter from getPCG1ofSigmaAndVector 1
AC 1541
S is 1.447213e-25
var1 is 1.178413e-10
p_exact 1
var2sparseGRM Here 1.184987e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1541
var1 1.178413e-10
var2null 1.178413e-10
var2null_noXadj 2.378183e-10
296 th marker in geno 1
MAC: 27
[1] "length(G0) aaaaa"
[1] 100
G0 0 0 0 1 0 0 0 0 0 0
[1] 4756 100
[1] 100
G0 0 0 0 0 0 0 0 0 0 0
CHR 22
V1 V2 V3 V4 V5 V6
2323 22 22_17197269_C_CT 0 17197269 C CT
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3283
iter from getPCG1ofSigmaAndVector 1
AC 1503
S is -7.842413e-25
var1 is 1.476646e-10
p_exact 1
var2sparseGRM Here 1.495282e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1503
var1 1.476646e-10
var2null 1.476646e-10
var2null_noXadj 2.055804e-10
35 th marker in geno 1
MAC: 23
[1] "length(G0) aaaaa"
[1] 100
G0 1 0 0 2 0 1 2 0 1 0
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 0
CHR 22
V1 V2 V3 V4 V5 V6
294 22 22_16724268_T_C 0 16724268 T C
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 3626
iter from getPCG1ofSigmaAndVector 1
AC 1168
S is -6.594877e-26
var1 is 1.191615e-10
p_exact 1
var2sparseGRM Here 1.211955e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 1168
var1 1.191615e-10
var2null 1.191615e-10
var2null_noXadj 1.79862e-10
100 th marker in geno 1
MAC: 84
[1] "length(G0) aaaaa"
[1] 100
G0 1 2 1 0 1 0 1 2 2 1
[1] 4756 100
[1] 100
G0 1 1 1 1 1 1 1 1 1 2
CHR 22
V1 V2 V3 V4 V5 V6
743 22 22_16851949_G_A 0 16851949 G A
[1] "length(G0)"
[1] 4756
[1] "length(NAset)"
[1] 1514
iter from getPCG1ofSigmaAndVector 1
AC 3886
S is 6.462222e-25
var1 is 2.308409e-10
p_exact 1
var2sparseGRM Here 2.391416e-10
mu
[1] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[6] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[11] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[16] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[21] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[26] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[31] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[36] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[41] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[46] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[51] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[56] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[61] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[66] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[71] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[76] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[81] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[86] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[91] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
[96] 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13 1.878836e-13
AC 3886
var1 2.308409e-10
var2null 2.308409e-10
var2null_noXadj 3.757012e-10
[1] "varRatio_NULL_vec"
[1] 0.9999999 0.9999999 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000
[8] 0.9999999 0.9999999 0.9999999 0.9999998 1.0000000 1.0000000 1.0000000
[15] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000
[22] 1.0000000 1.0000000 1.0000000 1.0000000 0.9999999 0.9999998 0.9999999
[29] 1.0000000 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 0.9999999
[36] 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000
[43] 0.9999999 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[50] 1.0000000 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000
[57] 0.9999999 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999997
[64] 1.0000000 1.0000000 0.9999999 1.0000000 0.9999998 1.0000000 1.0000000
[71] 1.0000000 1.0000000 1.0000000 0.9999998 1.0000000 0.9999999 1.0000000
[78] 1.0000000 0.9999999 1.0000000 1.0000000 1.0000000 1.0000000 1.0000000
[85] 1.0000000 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 1.0000000
[92] 0.9999998 0.9999999 1.0000000 0.9999999 1.0000000 0.9999999 1.0000000
[99] 1.0000000 0.9999999 0.9999999 0.9999999 1.0000000 0.9999999 1.0000000
[106] 0.9999998 1.0000000 0.9999999 0.9999998 0.9999999 1.0000000 1.0000000
[113] 1.0000000 0.9999999 0.9999999 1.0000000 1.0000000 0.9999998 1.0000000
[120] 0.9999999 1.0000000 1.0000000 0.9999999 0.9999999 0.9999999 1.0000000
[127] 1.0000000 1.0000000 1.0000000 0.9999999
[1] "varRatio_NULL_noXadj_vec"
[1] 0.7244184 0.6144269 0.7172815 0.4767569 0.5678297 0.5877695 0.6250880
[8] 0.5994013 0.5314215 0.7004979 0.5279262 0.5581007 0.5513605 0.5546946
[15] 0.5161837 0.6097295 0.5067370 0.5034013 0.5999383 0.5332749 0.4807181
[22] 0.6798313 0.6165431 0.5999383 0.7779147 0.5938738 0.6655329 0.6550868
[29] 0.6173393 0.7039355 0.7039355 0.7478727 0.5957820 0.7021776 0.5672443
[36] 0.6087334 0.5146316 0.5034013 0.5895097 0.7588943 0.6687631 0.6833148
[43] 0.5910448 0.5407933 0.6227349 0.8119943 0.6276360 0.6399538 0.5975857
[50] 0.5863973 0.7350271 0.5938738 0.5877695 0.5512501 0.5247584 0.5841749
[57] 0.5919259 0.8136709 0.5877695 0.6235232 0.6655329 0.5117239 0.5812990
[64] 0.7363415 0.7570300 0.6329186 0.6993860 0.7017279 0.6625159 0.4767569
[71] 0.4767569 0.6900629 0.5837497 0.5917542 0.6007226 0.5910448 0.5069967
[78] 0.5989036 0.6607730 0.4509542 0.5573382 0.5999383 0.7049514 0.7350271
[85] 0.6485165 0.7113415 0.6142823 0.5294457 0.5877695 0.5654688 0.5877424
[92] 0.5549693 0.5314215 0.6589600 0.6377957 0.5548297 0.5314215 0.7494220
[99] 0.5877424 0.5307448 0.6793402 0.6344690 0.6925500 0.4598288 0.5999383
[106] 0.5188123 0.6525936 0.5778247 0.5397307 0.4773059 0.4552038 0.7172815
[113] 0.5329297 0.6400785 0.6132442 0.5877424 0.6382745 0.6649785 0.6044509
[120] 0.5630728 0.5999383 0.6665186 0.6329186 0.5111809 0.5543179 0.5654688
[127] 0.4955099 0.7182814 0.6625159 0.6144269
CV for variance ratio estimate using 130 markers is 0.0009943061 < 0.001
varRatio_sparseGRM_vec
[1] 0.9935225 0.9652895 0.9682337 0.9903181 0.9910899 0.9967789 0.9733647
[8] 0.9821142 0.9887625 0.9916354 0.9909026 0.9901468 0.9772209 0.9749330
[15] 0.9829395 0.9877635 0.9936205 0.9495984 0.9921646 0.9935538 0.9878278
[22] 0.9962364 0.9947829 0.9921646 0.9822412 0.9935743 0.9807097 0.9929326
[29] 0.9946898 0.9923355 0.9923355 0.9853130 0.9928378 0.9862307 0.9744342
[36] 0.9879285 0.9907029 0.9495984 0.9905056 0.9923355 0.9812292 0.9912981
[43] 0.9906070 0.9936431 0.9922556 0.9945476 0.9932009 0.9799493 0.9862212
[50] 0.9869469 0.9794484 0.9935743 0.9967789 0.9891410 0.9506714 0.9834560
[57] 0.9953961 0.9896488 0.9967789 0.9922303 0.9807097 0.9914325 0.9825308
[64] 0.9920972 0.9948095 0.9902467 0.9954625 0.9903964 0.9832168 0.9903181
[71] 0.9903181 0.9948416 0.9924420 0.9739727 0.9719746 0.9906070 0.9918207
[78] 0.9821506 0.9816234 0.9901075 0.9938796 0.9921646 0.9854738 0.9794484
[85] 0.9712300 0.9873286 0.9877625 0.9893884 0.9967789 0.9928217 0.9738714
[92] 0.9723480 0.9887625 0.9487059 0.9852515 0.9908247 0.9887625 0.9913183
[99] 0.9738714 0.9934153 0.9665946 0.9892427 0.9897410 0.9909795 0.9921646
[106] 0.9914286 0.9681592 0.9814129 0.9925493 0.9924462 0.9743969 0.9682337
[113] 0.9857610 0.9951627 0.9656209 0.9738714 0.9901801 0.9935447 0.9756716
[120] 0.9736555 0.9921646 0.9820883 0.9902467 0.9928129 0.9910967 0.9928217
[127] 0.9944520 0.9875369 0.9832168 0.9652895
varRatio_sparse 0.9856748
varRatio_null 0.9999999
varRatio_null_noXadj 0.6083069
V1 V2 V3
1 0.9856748 sparse 1
2 0.9999999 null 1
3 0.6083069 null_noXadj 1
4 0.9856752 null_sample 1
[2026-01-09 01:41:14,395] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: optparse
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: RhpcBLASctl
warning: solve(): system is singular; attempting approx solution
Loading required package: fastSave
Warning messages:
1: glm.fit: algorithm did not converge
2: glm.fit: algorithm did not converge
3: glm.fit: algorithm did not converge
[2026-01-09 01:41:14,395] INFO:cellink.tl.external._saigeqtl: Running Step 2: Association tests
[2026-01-09 01:41:14,397] INFO:cellink.tl._runner: Executing: docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step2_tests_qtl.R --bedFile=saigeqtl_custom.bed --bimFile=saigeqtl_custom.bim --famFile=saigeqtl_custom.fam --GMMATmodelFile=saigeqtl_custom.rda --varianceRatioFile=saigeqtl_custom.varianceRatio.txt --SAIGEOutputFile=saigeqtl_custom_results.txt --minMAC=20 --LOCO=FALSE --rangestoIncludeFile=saigeqtl_custom_ranges.txt
[2026-01-09 01:41:31,069] INFO:cellink.tl._runner: R version 4.4.3 (2025-02-28)
Platform: x86_64-conda-linux-gnu
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS/LAPACK: /app/.pixi/envs/default/lib/libopenblasp-r0.3.30.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: NA
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.17.6 optparse_1.7.5 RhpcBLASctl_0.23-42
[4] SAIGEQTL_0.3.2
loaded via a namespace (and not attached):
[1] compiler_4.4.3 Matrix_1.7-3 Rcpp_1.1.0
[4] getopt_1.20.4 RcppNumerical_0.6-0 grid_4.4.3
[7] RcppParallel_5.1.9 lattice_0.22-7
$vcfFile
[1] ""
$vcfFileIndex
[1] ""
$vcfField
[1] "DS"
$savFile
[1] ""
$savFileIndex
[1] ""
$bgenFile
[1] ""
$bgenFileIndex
[1] ""
$sampleFile
[1] ""
$bedFile
[1] "saigeqtl_custom.bed"
$bimFile
[1] "saigeqtl_custom.bim"
$famFile
[1] "saigeqtl_custom.fam"
$AlleleOrder
[1] "alt-first"
$idstoIncludeFile
[1] ""
$rangestoIncludeFile
[1] "saigeqtl_custom_ranges.txt"
$chrom
[1] ""
$is_imputed_data
[1] FALSE
$minMAF
[1] 0
$minMAC
[1] 20
$minGroupMAC_in_BurdenTest
[1] 5
$minInfo
[1] 0
$maxMissing
[1] 0.15
$impute_method
[1] "best_guess"
$LOCO
[1] FALSE
$GMMATmodelFile
[1] "saigeqtl_custom.rda"
$varianceRatioFile
[1] "saigeqtl_custom.varianceRatio.txt"
$GMMATmodel_varianceRatio_multiTraits_File
[1] ""
$SAIGEOutputFile
[1] "saigeqtl_custom_results.txt"
$markers_per_chunk
[1] 10000
$groups_per_chunk
[1] 100
$is_output_moreDetails
[1] FALSE
$is_overwrite_output
[1] TRUE
$maxMAF_in_groupTest
[1] "0.0001,0.001,0.01"
$maxMAC_in_groupTest
[1] "0"
$annotation_in_groupTest
[1] "lof,missense;lof,missense;lof;synonymous"
$groupFile
[1] ""
$sparseGRMFile
[1] ""
$sparseGRMSampleIDFile
[1] ""
$relatednessCutoff
[1] 0
$MACCutoff_to_CollapseUltraRare
[1] 10
$cateVarRatioMinMACVecExclude
[1] "10,20.5"
$cateVarRatioMaxMACVecInclude
[1] "20.5"
$weights.beta
[1] "1;25"
$r.corr
[1] 0
$markers_per_chunk_in_groupTest
[1] 100
$condition
[1] ""
$SPAcutoff
[1] 2
$dosage_zerod_cutoff
[1] 0.2
$dosage_zerod_MAC_cutoff
[1] 10
$is_single_in_groupTest
[1] FALSE
$is_SKATO
[1] FALSE
$is_equal_weight_in_groupTest
[1] FALSE
$is_output_markerList_in_groupTest
[1] FALSE
$is_Firth_beta
[1] FALSE
$pCutoffforFirth
[1] 0.01
$is_fastTest
[1] FALSE
$is_noadjCov
[1] TRUE
$is_sparseGRM
[1] FALSE
$pval_cutoff_for_fastTest
[1] 0.05
$max_MAC_for_ER
[1] 4
$is_EmpSPA
[1] FALSE
$help
[1] FALSE
[1] "opt$r.corr"
[1] 0
dosage_zerod_cutoff 0.2
Any dosages <= 0.2 for genetic variants with MAC <= 10 are set to be 0 in group tests
single-variant association test will be performed
[1] "Leave-one-chromosome-out is not applied"
[1] "LOCO = FASLE and leave-one-chromosome-out is not applied"
isSparseGRM FALSE
variance Ratio null is 0.9999999
variance Ratio null_noXadj is 0.6083069
variance Ratio ratioVec_null_sample is 0.9856752
$ratioVec_sparse
[1] 0.9856748
$ratioVec_null
[1] 0.9999999
$ratioVec_null_sample
[1] 0.9856752
$ratioVec_null_noXadj
[1] 0.6083069
$ratioVec_null_eg
[1] -1
$ratioVec_sparse_eg
[1] -1
dosageFile type is plink
allele order in the plink file is alt-first .
Reading bim file....
Reading fam file....
Setting position of samples in PLINK files....
871 ranges are in rangestoIncludeFile
22 markers in the range 1 are found in the geno/dosage file.
1422 markers in the range 2 are found in the geno/dosage file.
1686 markers in the range 3 are found in the geno/dosage file.
1705 markers in the range 4 are found in the geno/dosage file.
1784 markers in the range 5 are found in the geno/dosage file.
2156 markers in the range 6 are found in the geno/dosage file.
2627 markers in the range 7 are found in the geno/dosage file.
2632 markers in the range 8 are found in the geno/dosage file.
2931 markers in the range 9 are found in the geno/dosage file.
3109 markers in the range 10 are found in the geno/dosage file.
3224 markers in the range 11 are found in the geno/dosage file.
3270 markers in the range 12 are found in the geno/dosage file.
3312 markers in the range 13 are found in the geno/dosage file.
3350 markers in the range 14 are found in the geno/dosage file.
3433 markers in the range 15 are found in the geno/dosage file.
3880 markers in the range 16 are found in the geno/dosage file.
4200 markers in the range 17 are found in the geno/dosage file.
4194 markers in the range 18 are found in the geno/dosage file.
4151 markers in the range 19 are found in the geno/dosage file.
4151 markers in the range 20 are found in the geno/dosage file.
4147 markers in the range 21 are found in the geno/dosage file.
4128 markers in the range 22 are found in the geno/dosage file.
4112 markers in the range 23 are found in the geno/dosage file.
3865 markers in the range 24 are found in the geno/dosage file.
3498 markers in the range 25 are found in the geno/dosage file.
2883 markers in the range 26 are found in the geno/dosage file.
2677 markers in the range 27 are found in the geno/dosage file.
2638 markers in the range 28 are found in the geno/dosage file.
2593 markers in the range 29 are found in the geno/dosage file.
2437 markers in the range 30 are found in the geno/dosage file.
1734 markers in the range 31 are found in the geno/dosage file.
1532 markers in the range 32 are found in the geno/dosage file.
1501 markers in the range 33 are found in the geno/dosage file.
1484 markers in the range 34 are found in the geno/dosage file.
492 markers in the range 35 are found in the geno/dosage file.
395 markers in the range 36 are found in the geno/dosage file.
256 markers in the range 37 are found in the geno/dosage file.
33 markers in the range 38 are found in the geno/dosage file.
17 markers in the range 39 are found in the geno/dosage file.
0 markers in the range 40 are found in the geno/dosage file.
0 markers in the range 41 are found in the geno/dosage file.
0 markers in the range 42 are found in the geno/dosage file.
0 markers in the range 43 are found in the geno/dosage file.
0 markers in the range 44 are found in the geno/dosage file.
0 markers in the range 45 are found in the geno/dosage file.
0 markers in the range 46 are found in the geno/dosage file.
0 markers in the range 47 are found in the geno/dosage file.
0 markers in the range 48 are found in the geno/dosage file.
0 markers in the range 49 are found in the geno/dosage file.
0 markers in the range 50 are found in the geno/dosage file.
0 markers in the range 51 are found in the geno/dosage file.
0 markers in the range 52 are found in the geno/dosage file.
0 markers in the range 53 are found in the geno/dosage file.
0 markers in the range 54 are found in the geno/dosage file.
0 markers in the range 55 are found in the geno/dosage file.
0 markers in the range 56 are found in the geno/dosage file.
0 markers in the range 57 are found in the geno/dosage file.
0 markers in the range 58 are found in the geno/dosage file.
0 markers in the range 59 are found in the geno/dosage file.
0 markers in the range 60 are found in the geno/dosage file.
0 markers in the range 61 are found in the geno/dosage file.
0 markers in the range 62 are found in the geno/dosage file.
0 markers in the range 63 are found in the geno/dosage file.
0 markers in the range 64 are found in the geno/dosage file.
0 markers in the range 65 are found in the geno/dosage file.
0 markers in the range 66 are found in the geno/dosage file.
0 markers in the range 67 are found in the geno/dosage file.
0 markers in the range 68 are found in the geno/dosage file.
0 markers in the range 69 are found in the geno/dosage file.
0 markers in the range 70 are found in the geno/dosage file.
0 markers in the range 71 are found in the geno/dosage file.
0 markers in the range 72 are found in the geno/dosage file.
0 markers in the range 73 are found in the geno/dosage file.
0 markers in the range 74 are found in the geno/dosage file.
0 markers in the range 75 are found in the geno/dosage file.
0 markers in the range 76 are found in the geno/dosage file.
0 markers in the range 77 are found in the geno/dosage file.
0 markers in the range 78 are found in the geno/dosage file.
0 markers in the range 79 are found in the geno/dosage file.
0 markers in the range 80 are found in the geno/dosage file.
0 markers in the range 81 are found in the geno/dosage file.
0 markers in the range 82 are found in the geno/dosage file.
0 markers in the range 83 are found in the geno/dosage file.
0 markers in the range 84 are found in the geno/dosage file.
0 markers in the range 85 are found in the geno/dosage file.
0 markers in the range 86 are found in the geno/dosage file.
0 markers in the range 87 are found in the geno/dosage file.
0 markers in the range 88 are found in the geno/dosage file.
0 markers in the range 89 are found in the geno/dosage file.
0 markers in the range 90 are found in the geno/dosage file.
0 markers in the range 91 are found in the geno/dosage file.
0 markers in the range 92 are found in the geno/dosage file.
0 markers in the range 93 are found in the geno/dosage file.
0 markers in the range 94 are found in the geno/dosage file.
0 markers in the range 95 are found in the geno/dosage file.
0 markers in the range 96 are found in the geno/dosage file.
0 markers in the range 97 are found in the geno/dosage file.
0 markers in the range 98 are found in the geno/dosage file.
0 markers in the range 99 are found in the geno/dosage file.
0 markers in the range 100 are found in the geno/dosage file.
0 markers in the range 101 are found in the geno/dosage file.
0 markers in the range 102 are found in the geno/dosage file.
0 markers in the range 103 are found in the geno/dosage file.
0 markers in the range 104 are found in the geno/dosage file.
0 markers in the range 105 are found in the geno/dosage file.
0 markers in the range 106 are found in the geno/dosage file.
0 markers in the range 107 are found in the geno/dosage file.
0 markers in the range 108 are found in the geno/dosage file.
0 markers in the range 109 are found in the geno/dosage file.
0 markers in the range 110 are found in the geno/dosage file.
0 markers in the range 111 are found in the geno/dosage file.
0 markers in the range 112 are found in the geno/dosage file.
0 markers in the range 113 are found in the geno/dosage file.
0 markers in the range 114 are found in the geno/dosage file.
0 markers in the range 115 are found in the geno/dosage file.
0 markers in the range 116 are found in the geno/dosage file.
0 markers in the range 117 are found in the geno/dosage file.
0 markers in the range 118 are found in the geno/dosage file.
0 markers in the range 119 are found in the geno/dosage file.
0 markers in the range 120 are found in the geno/dosage file.
0 markers in the range 121 are found in the geno/dosage file.
0 markers in the range 122 are found in the geno/dosage file.
0 markers in the range 123 are found in the geno/dosage file.
0 markers in the range 124 are found in the geno/dosage file.
0 markers in the range 125 are found in the geno/dosage file.
0 markers in the range 126 are found in the geno/dosage file.
0 markers in the range 127 are found in the geno/dosage file.
0 markers in the range 128 are found in the geno/dosage file.
0 markers in the range 129 are found in the geno/dosage file.
0 markers in the range 130 are found in the geno/dosage file.
0 markers in the range 131 are found in the geno/dosage file.
0 markers in the range 132 are found in the geno/dosage file.
0 markers in the range 133 are found in the geno/dosage file.
0 markers in the range 134 are found in the geno/dosage file.
0 markers in the range 135 are found in the geno/dosage file.
0 markers in the range 136 are found in the geno/dosage file.
0 markers in the range 137 are found in the geno/dosage file.
0 markers in the range 138 are found in the geno/dosage file.
0 markers in the range 139 are found in the geno/dosage file.
0 markers in the range 140 are found in the geno/dosage file.
0 markers in the range 141 are found in the geno/dosage file.
0 markers in the range 142 are found in the geno/dosage file.
0 markers in the range 143 are found in the geno/dosage file.
0 markers in the range 144 are found in the geno/dosage file.
0 markers in the range 145 are found in the geno/dosage file.
0 markers in the range 146 are found in the geno/dosage file.
0 markers in the range 147 are found in the geno/dosage file.
0 markers in the range 148 are found in the geno/dosage file.
0 markers in the range 149 are found in the geno/dosage file.
0 markers in the range 150 are found in the geno/dosage file.
0 markers in the range 151 are found in the geno/dosage file.
0 markers in the range 152 are found in the geno/dosage file.
0 markers in the range 153 are found in the geno/dosage file.
0 markers in the range 154 are found in the geno/dosage file.
0 markers in the range 155 are found in the geno/dosage file.
0 markers in the range 156 are found in the geno/dosage file.
0 markers in the range 157 are found in the geno/dosage file.
0 markers in the range 158 are found in the geno/dosage file.
0 markers in the range 159 are found in the geno/dosage file.
0 markers in the range 160 are found in the geno/dosage file.
0 markers in the range 161 are found in the geno/dosage file.
0 markers in the range 162 are found in the geno/dosage file.
0 markers in the range 163 are found in the geno/dosage file.
0 markers in the range 164 are found in the geno/dosage file.
0 markers in the range 165 are found in the geno/dosage file.
0 markers in the range 166 are found in the geno/dosage file.
0 markers in the range 167 are found in the geno/dosage file.
0 markers in the range 168 are found in the geno/dosage file.
0 markers in the range 169 are found in the geno/dosage file.
0 markers in the range 170 are found in the geno/dosage file.
0 markers in the range 171 are found in the geno/dosage file.
0 markers in the range 172 are found in the geno/dosage file.
0 markers in the range 173 are found in the geno/dosage file.
0 markers in the range 174 are found in the geno/dosage file.
0 markers in the range 175 are found in the geno/dosage file.
0 markers in the range 176 are found in the geno/dosage file.
0 markers in the range 177 are found in the geno/dosage file.
0 markers in the range 178 are found in the geno/dosage file.
0 markers in the range 179 are found in the geno/dosage file.
0 markers in the range 180 are found in the geno/dosage file.
0 markers in the range 181 are found in the geno/dosage file.
0 markers in the range 182 are found in the geno/dosage file.
0 markers in the range 183 are found in the geno/dosage file.
0 markers in the range 184 are found in the geno/dosage file.
0 markers in the range 185 are found in the geno/dosage file.
0 markers in the range 186 are found in the geno/dosage file.
0 markers in the range 187 are found in the geno/dosage file.
0 markers in the range 188 are found in the geno/dosage file.
0 markers in the range 189 are found in the geno/dosage file.
0 markers in the range 190 are found in the geno/dosage file.
0 markers in the range 191 are found in the geno/dosage file.
0 markers in the range 192 are found in the geno/dosage file.
0 markers in the range 193 are found in the geno/dosage file.
0 markers in the range 194 are found in the geno/dosage file.
0 markers in the range 195 are found in the geno/dosage file.
0 markers in the range 196 are found in the geno/dosage file.
0 markers in the range 197 are found in the geno/dosage file.
0 markers in the range 198 are found in the geno/dosage file.
0 markers in the range 199 are found in the geno/dosage file.
0 markers in the range 200 are found in the geno/dosage file.
0 markers in the range 201 are found in the geno/dosage file.
0 markers in the range 202 are found in the geno/dosage file.
0 markers in the range 203 are found in the geno/dosage file.
0 markers in the range 204 are found in the geno/dosage file.
0 markers in the range 205 are found in the geno/dosage file.
0 markers in the range 206 are found in the geno/dosage file.
0 markers in the range 207 are found in the geno/dosage file.
0 markers in the range 208 are found in the geno/dosage file.
0 markers in the range 209 are found in the geno/dosage file.
0 markers in the range 210 are found in the geno/dosage file.
0 markers in the range 211 are found in the geno/dosage file.
0 markers in the range 212 are found in the geno/dosage file.
0 markers in the range 213 are found in the geno/dosage file.
0 markers in the range 214 are found in the geno/dosage file.
0 markers in the range 215 are found in the geno/dosage file.
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0 markers in the range 643 are found in the geno/dosage file.
0 markers in the range 644 are found in the geno/dosage file.
0 markers in the range 645 are found in the geno/dosage file.
0 markers in the range 646 are found in the geno/dosage file.
0 markers in the range 647 are found in the geno/dosage file.
0 markers in the range 648 are found in the geno/dosage file.
0 markers in the range 649 are found in the geno/dosage file.
0 markers in the range 650 are found in the geno/dosage file.
0 markers in the range 651 are found in the geno/dosage file.
0 markers in the range 652 are found in the geno/dosage file.
0 markers in the range 653 are found in the geno/dosage file.
0 markers in the range 654 are found in the geno/dosage file.
0 markers in the range 655 are found in the geno/dosage file.
0 markers in the range 656 are found in the geno/dosage file.
0 markers in the range 657 are found in the geno/dosage file.
0 markers in the range 658 are found in the geno/dosage file.
0 markers in the range 659 are found in the geno/dosage file.
0 markers in the range 660 are found in the geno/dosage file.
0 markers in the range 661 are found in the geno/dosage file.
0 markers in the range 662 are found in the geno/dosage file.
0 markers in the range 663 are found in the geno/dosage file.
0 markers in the range 664 are found in the geno/dosage file.
0 markers in the range 665 are found in the geno/dosage file.
0 markers in the range 666 are found in the geno/dosage file.
0 markers in the range 667 are found in the geno/dosage file.
0 markers in the range 668 are found in the geno/dosage file.
0 markers in the range 669 are found in the geno/dosage file.
0 markers in the range 670 are found in the geno/dosage file.
0 markers in the range 671 are found in the geno/dosage file.
0 markers in the range 672 are found in the geno/dosage file.
0 markers in the range 673 are found in the geno/dosage file.
0 markers in the range 674 are found in the geno/dosage file.
0 markers in the range 675 are found in the geno/dosage file.
0 markers in the range 676 are found in the geno/dosage file.
0 markers in the range 677 are found in the geno/dosage file.
0 markers in the range 678 are found in the geno/dosage file.
0 markers in the range 679 are found in the geno/dosage file.
0 markers in the range 680 are found in the geno/dosage file.
0 markers in the range 681 are found in the geno/dosage file.
0 markers in the range 682 are found in the geno/dosage file.
0 markers in the range 683 are found in the geno/dosage file.
0 markers in the range 684 are found in the geno/dosage file.
0 markers in the range 685 are found in the geno/dosage file.
0 markers in the range 686 are found in the geno/dosage file.
0 markers in the range 687 are found in the geno/dosage file.
0 markers in the range 688 are found in the geno/dosage file.
0 markers in the range 689 are found in the geno/dosage file.
0 markers in the range 690 are found in the geno/dosage file.
0 markers in the range 691 are found in the geno/dosage file.
0 markers in the range 692 are found in the geno/dosage file.
0 markers in the range 693 are found in the geno/dosage file.
0 markers in the range 694 are found in the geno/dosage file.
0 markers in the range 695 are found in the geno/dosage file.
0 markers in the range 696 are found in the geno/dosage file.
0 markers in the range 697 are found in the geno/dosage file.
0 markers in the range 698 are found in the geno/dosage file.
0 markers in the range 699 are found in the geno/dosage file.
0 markers in the range 700 are found in the geno/dosage file.
0 markers in the range 701 are found in the geno/dosage file.
0 markers in the range 702 are found in the geno/dosage file.
0 markers in the range 703 are found in the geno/dosage file.
0 markers in the range 704 are found in the geno/dosage file.
0 markers in the range 705 are found in the geno/dosage file.
0 markers in the range 706 are found in the geno/dosage file.
0 markers in the range 707 are found in the geno/dosage file.
0 markers in the range 708 are found in the geno/dosage file.
0 markers in the range 709 are found in the geno/dosage file.
0 markers in the range 710 are found in the geno/dosage file.
0 markers in the range 711 are found in the geno/dosage file.
0 markers in the range 712 are found in the geno/dosage file.
0 markers in the range 713 are found in the geno/dosage file.
0 markers in the range 714 are found in the geno/dosage file.
0 markers in the range 715 are found in the geno/dosage file.
0 markers in the range 716 are found in the geno/dosage file.
0 markers in the range 717 are found in the geno/dosage file.
0 markers in the range 718 are found in the geno/dosage file.
0 markers in the range 719 are found in the geno/dosage file.
0 markers in the range 720 are found in the geno/dosage file.
0 markers in the range 721 are found in the geno/dosage file.
0 markers in the range 722 are found in the geno/dosage file.
0 markers in the range 723 are found in the geno/dosage file.
0 markers in the range 724 are found in the geno/dosage file.
0 markers in the range 725 are found in the geno/dosage file.
0 markers in the range 726 are found in the geno/dosage file.
0 markers in the range 727 are found in the geno/dosage file.
0 markers in the range 728 are found in the geno/dosage file.
0 markers in the range 729 are found in the geno/dosage file.
0 markers in the range 730 are found in the geno/dosage file.
0 markers in the range 731 are found in the geno/dosage file.
0 markers in the range 732 are found in the geno/dosage file.
0 markers in the range 733 are found in the geno/dosage file.
0 markers in the range 734 are found in the geno/dosage file.
0 markers in the range 735 are found in the geno/dosage file.
0 markers in the range 736 are found in the geno/dosage file.
0 markers in the range 737 are found in the geno/dosage file.
0 markers in the range 738 are found in the geno/dosage file.
0 markers in the range 739 are found in the geno/dosage file.
0 markers in the range 740 are found in the geno/dosage file.
0 markers in the range 741 are found in the geno/dosage file.
0 markers in the range 742 are found in the geno/dosage file.
0 markers in the range 743 are found in the geno/dosage file.
0 markers in the range 744 are found in the geno/dosage file.
0 markers in the range 745 are found in the geno/dosage file.
0 markers in the range 746 are found in the geno/dosage file.
0 markers in the range 747 are found in the geno/dosage file.
0 markers in the range 748 are found in the geno/dosage file.
0 markers in the range 749 are found in the geno/dosage file.
0 markers in the range 750 are found in the geno/dosage file.
0 markers in the range 751 are found in the geno/dosage file.
0 markers in the range 752 are found in the geno/dosage file.
0 markers in the range 753 are found in the geno/dosage file.
0 markers in the range 754 are found in the geno/dosage file.
0 markers in the range 755 are found in the geno/dosage file.
0 markers in the range 756 are found in the geno/dosage file.
0 markers in the range 757 are found in the geno/dosage file.
0 markers in the range 758 are found in the geno/dosage file.
0 markers in the range 759 are found in the geno/dosage file.
0 markers in the range 760 are found in the geno/dosage file.
0 markers in the range 761 are found in the geno/dosage file.
0 markers in the range 762 are found in the geno/dosage file.
0 markers in the range 763 are found in the geno/dosage file.
0 markers in the range 764 are found in the geno/dosage file.
0 markers in the range 765 are found in the geno/dosage file.
0 markers in the range 766 are found in the geno/dosage file.
0 markers in the range 767 are found in the geno/dosage file.
0 markers in the range 768 are found in the geno/dosage file.
0 markers in the range 769 are found in the geno/dosage file.
0 markers in the range 770 are found in the geno/dosage file.
0 markers in the range 771 are found in the geno/dosage file.
0 markers in the range 772 are found in the geno/dosage file.
0 markers in the range 773 are found in the geno/dosage file.
0 markers in the range 774 are found in the geno/dosage file.
0 markers in the range 775 are found in the geno/dosage file.
0 markers in the range 776 are found in the geno/dosage file.
0 markers in the range 777 are found in the geno/dosage file.
0 markers in the range 778 are found in the geno/dosage file.
0 markers in the range 779 are found in the geno/dosage file.
0 markers in the range 780 are found in the geno/dosage file.
0 markers in the range 781 are found in the geno/dosage file.
0 markers in the range 782 are found in the geno/dosage file.
0 markers in the range 783 are found in the geno/dosage file.
0 markers in the range 784 are found in the geno/dosage file.
0 markers in the range 785 are found in the geno/dosage file.
0 markers in the range 786 are found in the geno/dosage file.
0 markers in the range 787 are found in the geno/dosage file.
0 markers in the range 788 are found in the geno/dosage file.
0 markers in the range 789 are found in the geno/dosage file.
0 markers in the range 790 are found in the geno/dosage file.
0 markers in the range 791 are found in the geno/dosage file.
0 markers in the range 792 are found in the geno/dosage file.
0 markers in the range 793 are found in the geno/dosage file.
0 markers in the range 794 are found in the geno/dosage file.
0 markers in the range 795 are found in the geno/dosage file.
0 markers in the range 796 are found in the geno/dosage file.
0 markers in the range 797 are found in the geno/dosage file.
0 markers in the range 798 are found in the geno/dosage file.
0 markers in the range 799 are found in the geno/dosage file.
0 markers in the range 800 are found in the geno/dosage file.
0 markers in the range 801 are found in the geno/dosage file.
0 markers in the range 802 are found in the geno/dosage file.
0 markers in the range 803 are found in the geno/dosage file.
0 markers in the range 804 are found in the geno/dosage file.
0 markers in the range 805 are found in the geno/dosage file.
0 markers in the range 806 are found in the geno/dosage file.
0 markers in the range 807 are found in the geno/dosage file.
0 markers in the range 808 are found in the geno/dosage file.
0 markers in the range 809 are found in the geno/dosage file.
0 markers in the range 810 are found in the geno/dosage file.
0 markers in the range 811 are found in the geno/dosage file.
0 markers in the range 812 are found in the geno/dosage file.
0 markers in the range 813 are found in the geno/dosage file.
0 markers in the range 814 are found in the geno/dosage file.
0 markers in the range 815 are found in the geno/dosage file.
0 markers in the range 816 are found in the geno/dosage file.
0 markers in the range 817 are found in the geno/dosage file.
0 markers in the range 818 are found in the geno/dosage file.
0 markers in the range 819 are found in the geno/dosage file.
0 markers in the range 820 are found in the geno/dosage file.
0 markers in the range 821 are found in the geno/dosage file.
0 markers in the range 822 are found in the geno/dosage file.
0 markers in the range 823 are found in the geno/dosage file.
0 markers in the range 824 are found in the geno/dosage file.
0 markers in the range 825 are found in the geno/dosage file.
0 markers in the range 826 are found in the geno/dosage file.
0 markers in the range 827 are found in the geno/dosage file.
0 markers in the range 828 are found in the geno/dosage file.
0 markers in the range 829 are found in the geno/dosage file.
0 markers in the range 830 are found in the geno/dosage file.
0 markers in the range 831 are found in the geno/dosage file.
0 markers in the range 832 are found in the geno/dosage file.
0 markers in the range 833 are found in the geno/dosage file.
0 markers in the range 834 are found in the geno/dosage file.
0 markers in the range 835 are found in the geno/dosage file.
0 markers in the range 836 are found in the geno/dosage file.
0 markers in the range 837 are found in the geno/dosage file.
0 markers in the range 838 are found in the geno/dosage file.
0 markers in the range 839 are found in the geno/dosage file.
0 markers in the range 840 are found in the geno/dosage file.
0 markers in the range 841 are found in the geno/dosage file.
0 markers in the range 842 are found in the geno/dosage file.
0 markers in the range 843 are found in the geno/dosage file.
0 markers in the range 844 are found in the geno/dosage file.
0 markers in the range 845 are found in the geno/dosage file.
0 markers in the range 846 are found in the geno/dosage file.
0 markers in the range 847 are found in the geno/dosage file.
0 markers in the range 848 are found in the geno/dosage file.
0 markers in the range 849 are found in the geno/dosage file.
0 markers in the range 850 are found in the geno/dosage file.
0 markers in the range 851 are found in the geno/dosage file.
0 markers in the range 852 are found in the geno/dosage file.
0 markers in the range 853 are found in the geno/dosage file.
0 markers in the range 854 are found in the geno/dosage file.
0 markers in the range 855 are found in the geno/dosage file.
0 markers in the range 856 are found in the geno/dosage file.
0 markers in the range 857 are found in the geno/dosage file.
0 markers in the range 858 are found in the geno/dosage file.
0 markers in the range 859 are found in the geno/dosage file.
0 markers in the range 860 are found in the geno/dosage file.
0 markers in the range 861 are found in the geno/dosage file.
0 markers in the range 862 are found in the geno/dosage file.
0 markers in the range 863 are found in the geno/dosage file.
0 markers in the range 864 are found in the geno/dosage file.
0 markers in the range 865 are found in the geno/dosage file.
0 markers in the range 866 are found in the geno/dosage file.
0 markers in the range 867 are found in the geno/dosage file.
0 markers in the range 868 are found in the geno/dosage file.
0 markers in the range 869 are found in the geno/dosage file.
0 markers in the range 870 are found in the geno/dosage file.
0 markers in the range 871 are found in the geno/dosage file.
[1] 100 100
isSparseGRM 2 TRUE
pval_cutoff_for_gxe 0.001
traitType count
Number of phenotypes to test: 1
Number of all markers to test: 4277
Number of markers in each chunk: 10000
Number of chunks for all markers: 1
(2026-01-09 00:41:30.813628) ---- Analyzing Chunk 1/1: chrom InitialChunk ----
2433 markers were tested.
write to output
user system elapsed
14.070 2.292 16.250
[1] "Analysis done! The results have been saved to 'saigeqtl_custom_results.txt'."
[2026-01-09 01:41:31,070] WARNING:cellink.tl._runner: WARNING: The requested image's platform (linux/amd64) does not match the detected host platform (linux/arm64/v8) and no specific platform was requested
Loading required package: RhpcBLASctl
Warning: Your system is mis-configured: ‘/var/db/timezone/localtime’ is not a symlink
Warning: ‘/var/db/timezone/localtime’ is not identical to any known timezone file
Loading required package: furrr
Loading required package: future
| CHR | POS | MarkerID | Allele1 | Allele2 | AC_Allele2 | AF_Allele2 | MissingRate | BETA | SE | Tstat | var | p.value | p.value.NA | Is.SPA | N | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 22 | 16569715 | 22_16569715_G_A | A | G | 106 | 0.530 | 0 | -1.287330e-15 | 54527.0 | -4.329770e-25 | 3.363390e-10 | 1 | 1 | False | 100 |
| 1 | 22 | 16569887 | 22_16569887_T_A | A | T | 133 | 0.665 | 0 | -1.732230e-16 | 61881.1 | -4.523640e-26 | 2.611460e-10 | 1 | 1 | False | 100 |
| 2 | 22 | 16570090 | 22_16570090_ACATT_A | A | ACATT | 151 | 0.755 | 0 | -3.843350e-16 | 70399.5 | -7.754820e-26 | 2.017720e-10 | 1 | 1 | False | 100 |
| 3 | 22 | 16570885 | 22_16570885_T_G | G | T | 141 | 0.705 | 0 | -1.066060e-16 | 64219.4 | -2.584940e-26 | 2.424750e-10 | 1 | 1 | False | 100 |
| 4 | 22 | 16571233 | 22_16571233_G_A | A | G | 101 | 0.505 | 0 | -1.350560e-15 | 57144.1 | -4.135900e-25 | 3.062370e-10 | 1 | 1 | False | 100 |
Advanced Usage: Dry Run and Command Generation#
Generate Commands Without Execution#
Useful for debugging or running on HPC clusters:
# Generate command strings without executing
commands = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="saigeqtl_cluster",
mode="cis",
window=cis_window,
sample_covariates=["gPCs"],
use_grm_to_fit_null=False,
overwrite_variance_ratio_file=True,
run=False, # Don't execute, just return commands
)
print("Step 1 (Null model):")
print(commands["step1"])
print("\nStep 2 (Association tests):")
print(commands["step2"])
Writing FAM... done.
Writing BIM... done.
Step 1 (Null model):
docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step1_fitNULLGLMM_qtl.R --phenoFile=saigeqtl_cluster_phenotype.txt --phenoCol=ENSG00000273362 --sampleIDColinphenoFile=IND_ID --traitType=count --plinkFile=saigeqtl_cluster --outputPrefix=saigeqtl_cluster --LOCO=FALSE --useGRMtoFitNULL=FALSE --IsOverwriteVarianceRatioFile=TRUE --covarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19 --sampleCovarColList=sex,age,gPCs_0,gPCs_1,gPCs_2,gPCs_3,gPCs_4,gPCs_5,gPCs_6,gPCs_7,gPCs_8,gPCs_9,gPCs_10,gPCs_11,gPCs_12,gPCs_13,gPCs_14,gPCs_15,gPCs_16,gPCs_17,gPCs_18,gPCs_19
Step 2 (Association tests):
docker run --rm -v /Users/larnoldt/sc-genetics/docs/tutorials:/data -v /Users/larnoldt/cellink_data:/cellink_data -w /data wzhou88/saigeqtl /app/.pixi/envs/default/bin/Rscript /app/extdata/step2_tests_qtl.R --bedFile=saigeqtl_cluster.bed --bimFile=saigeqtl_cluster.bim --famFile=saigeqtl_cluster.fam --GMMATmodelFile=saigeqtl_cluster.rda --varianceRatioFile=saigeqtl_cluster.varianceRatio.txt --SAIGEOutputFile=saigeqtl_cluster_results.txt --minMAC=20 --LOCO=FALSE --rangestoIncludeFile=saigeqtl_cluster_ranges.txt
Save Commands to File#
For batch submission to compute clusters:
commands = run_saigeqtl(
dd,
gene_col="ENSG00000273362",
prefix="saigeqtl_batch",
mode="cis",
window=cis_window,
sample_covariates=["gPCs"],
run=False,
use_grm_to_fit_null=False,
overwrite_variance_ratio_file=True,
save_cmd_file="saigeqtl_job.sh",
)
Writing FAM... done.
Writing BIM... done.