Tutorial: Colocalization Analysis - Linking eQTLs to GWAS Signals with cellink#
This tutorial demonstrates how to perform colocalization analysis to determine whether eQTL signals and GWAS signals share the same causal variant. Colocalization is a powerful approach for interpreting GWAS results by identifying the specific genes and cell types through which genetic variants influence disease risk. When a GWAS identifies a disease-associated locus, the causal mechanism is often unclear. Colocalization analysis tests whether an eQTL signal and a GWAS signal in the same region are driven by the same causal variant (colocalization) or they represent independent association signals that happen to be nearby (linkage).
We’ll use the coloc method, a Bayesian approach that calculates posterior probabilities for different colocalization scenarios. You need to install the R package coloc. This tutorial assumes you’ve completed earlier tutorials on eQTL analysis and have familiarity with GWAS summary statistics. The cellink package provides convenient wrapper functions fpr TensorQTL, which we use for eQTL mapping here. To use TensorQTL you can install it via pip install 'cellink[tensorqtl]'. TensorQTL also requires plink2. For visualization of QTL calling results, please consider checking out the Tutorial: Pseudobulk eQTL Analysis with cellink.
Environment Setup#
We begin by importing necessary libraries and defining parameters for colocalization analysis.
import numpy as np
import pandas as pd
from cellink.resources import get_dummy_onek1k, get_gwas_catalog_study_summary_stats
from cellink.tl.external import run_tensorqtl
import rpy2.robjects as ro
from rpy2.robjects import pandas2ri
from rpy2.robjects.packages import importr
coloc = importr("coloc")
pandas2ri.activate()
import matplotlib.pyplot as plt
import seaborn as sns
sns.set_style("whitegrid")
# Analysis parameters
chrom = 22
cis_window = 500_000
cell_type = "CD16 Mono"
celltype_key = "predicted.celltype.l2"
original_donor_col = "donor_id"
n_gpcs = 20
pb_gex_key = f"PB_{cell_type}"
# Colocalization parameters
coloc_p1 = 1e-4 # Prior probability a SNP is associated with trait 1
coloc_p2 = 1e-4 # Prior probability a SNP is associated with trait 2
coloc_p12 = 1e-5 # Prior probability a SNP is associated with both traits
[2025-12-30 00:44:38,429] INFO:rpy2.situation: cffi mode is CFFI_MODE.ANY
[2025-12-30 00:44:38,486] INFO:rpy2.situation: R home found: /opt/miniconda3/envs/tensorqtl_jaxqtl/lib/R
[2025-12-30 00:44:38,782] INFO:rpy2.situation: R library path:
[2025-12-30 00:44:38,782] INFO:rpy2.situation: LD_LIBRARY_PATH:
[2025-12-30 00:44:38,787] INFO:rpy2.rinterface_lib.embedded: Default options to initialize R: rpy2, --quiet, --no-save
[2025-12-30 00:44:38,994] INFO:rpy2.rinterface_lib.embedded: R is already initialized. No need to initialize.
Load and Prepare eQTL Data#
First, we’ll generate eQTL results using TensorQTL. If you already have eQTL results from previous tutorials, you can skip this section and load your existing 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]]
[2025-12-30 00:44:39,981] INFO:root: /Users/larnoldt/cellink_data/dummy_onek1k/dummy_onek1k.dd.h5 already exists
[2025-12-30 00:44:39,982] WARNING:root: No checksum provided, skipping verification
[2025-12-30 00:44:41,205] INFO:root: Loaded dummy OneK1K dataset: (100, 146939, 125366, 34073)
Dataset shape: (100, 146939, 125366, 34073)
dd.aggregate(obs=["donor_id", "sex", "age"], func="first", add_to_obs=True)
# Filter to specific cell type
dd = dd[..., dd.C.obs[celltype_key] == cell_type, :].copy()
print(f"After cell type filtering: {dd.shape}")
# Add donor-level metadata
dd.G.obs["donor_sex"] = dd.G.obs["sex"]
dd.G.obs["donor_age"] = dd.G.obs["age"]
# Generate random labels for demonstration (replace with real phenotypes)
dd.G.obs["donor_labels"] = np.random.randint(2, size=len(dd.G.obs))
# Filter to specific chromosome for faster analysis
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}")
After cell type filtering: (90, 146939, 1486, 34073)
After chromosome 22 filtering: (90, 136776, 1486, 871)
Run TensorQTL Nominal Analysis#
We’ll use TensorQTL’s nominal mode to get association statistics for all variant-gene pairs, which we’ll need for colocalization.
results_tensorqtl = run_tensorqtl(
dd,
prefix="colocalization_eqtl",
mode="cis_nominal",
window=cis_window,
additional_covariates=["gPCs"],
batch_size=20000,
run=True,
)
cis_qtl_pairs = results_tensorqtl[0]
print(f"Total variant-gene pairs: {len(cis_qtl_pairs)}")
print(f"Columns: {cis_qtl_pairs.columns.tolist()}")
cis_qtl_pairs.head()
[2025-12-30 00:44:41,510] INFO:cellink._core.donordata: Aggregated X to PB
[2025-12-30 00:44:41,511] INFO:cellink._core.donordata: Observation found for 90 donors.
[2025-12-30 00:44:41,652] INFO:cellink.tl.external._tensorqtl: Performing z-normalization of age.
Writing FAM... done.
Writing BIM...
done.
PLINK v2.0.0-a.6.9 64-bit (29 Jan 2025) cog-genomics.org/plink/2.0/
(C) 2005-2025 Shaun Purcell, Christopher Chang GNU General Public License v3
Logging to colocalization_eqtl.log.
Options in effect:
--bfile colocalization_eqtl
--make-pgen
--out colocalization_eqtl
Start time: Tue Dec 30 00:44:42 2025
24576 MiB RAM detected; reserving 12288 MiB for main workspace.
Using up to 8 compute threads.
90 samples (0 females, 34 males, 56 ambiguous; 90 founders) loaded from
colocalization_eqtl.fam.
136776 variants loaded from colocalization_eqtl.bim.
Note: No phenotype data present.
Writing colocalization_eqtl.psam ... done.
Writing colocalization_eqtl.pvar ... 1010111112121313141415151616171718181919202021212222232324252526262727282829293030313132323333343435353636373738383939404041414242434344444545464647474848495050515152525353545455555656575758585959606061616262636364646565666667676868696970707171727273737475757676777778787979808081818282838384848585868687878888898990909191929293939494959596969797989899done.
Writing colocalization_eqtl.pgen ... done.
End time: Tue Dec 30 00:44:42 2025
[Dec 30 00:44:46] Running TensorQTL v1.0.10: cis-QTL mapping
* WARNING: using CPU!
* reading phenotypes (colocalization_eqtl_phenotype.bed.gz)
* cis-window detected as [start - 500,000, end + 500,000]
* reading covariates (colocalization_eqtl_donor_features.tsv)
* loading genotypes
cis-QTL mapping: nominal associations for all variant-phenotype pairs
* 90 samples
* 871 phenotypes
* 23 covariates
* 136776 variants
* cis-window: ±500,000
** dropping 425 constant phenotypes
* checking phenotypes: 446/446
* Computing associations
Mapping chromosome 22
processing phenotype 446/446
time elapsed: 0.03 min
* writing output
done.
[Dec 30 00:44:49] Finished mapping
Total variant-gene pairs: 1737760
Columns: ['phenotype_id', 'variant_id', 'start_distance', 'end_distance', 'af', 'ma_samples', 'ma_count', 'pval_nominal', 'slope', 'slope_se']
| phenotype_id | variant_id | start_distance | end_distance | af | ma_samples | ma_count | pval_nominal | slope | slope_se | |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | ENSG00000177663 | 22_16585130_T_C | -499825 | -530563 | 0.977778 | 4 | 4 | 0.706084 | -0.065519 | 0.172973 |
| 1 | ENSG00000177663 | 22_16585144_G_A | -499811 | -530549 | 0.905556 | 15 | 17 | 0.969395 | -0.002678 | 0.069540 |
| 2 | ENSG00000177663 | 22_16585510_C_G | -499445 | -530183 | 0.483333 | 62 | 87 | 0.436520 | 0.031384 | 0.040086 |
| 3 | ENSG00000177663 | 22_16585603_G_A | -499352 | -530090 | 0.744444 | 39 | 46 | 0.906565 | 0.005665 | 0.048079 |
| 4 | ENSG00000177663 | 22_16585810_T_C | -499145 | -529883 | 0.727778 | 38 | 49 | 0.476285 | -0.033120 | 0.046229 |
cis_qtl_pairs = cis_qtl_pairs[~cis_qtl_pairs["slope"].isna()]
Parse and Format eQTL Results#
We’ll organize the eQTL results by gene for easier colocalization analysis.
def prepare_eqtl_for_coloc(eqtl_results, gene_id):
"""
Prepare eQTL results for a specific gene for coloc analysis.
Parameters
----------
eqtl_results : pd.DataFrame
TensorQTL nominal output
gene_id : str
Gene identifier
Returns
-------
pd.DataFrame
Formatted results with required columns
"""
gene_data = eqtl_results[eqtl_results["phenotype_id"] == gene_id].copy()
if len(gene_data) == 0:
return None
gene_data = gene_data.rename(
columns={"variant_id": "SNP", "pval_nominal": "pvalue", "slope": "beta", "slope_se": "se"}
)
gene_data["varbeta"] = gene_data["se"] ** 2
gene_data[["chr", "pos", "ref", "alt"]] = gene_data["SNP"].str.split("_", expand=True)
gene_data["pos"] = gene_data["pos"].astype(int)
return gene_data[["SNP", "chr", "pos", "ref", "alt", "beta", "varbeta", "pvalue"]]
example_gene = cis_qtl_pairs["phenotype_id"].iloc[0]
eqtl_formatted = prepare_eqtl_for_coloc(cis_qtl_pairs, example_gene)
print(f"\nFormatted eQTL data for {example_gene}:")
print(f"Variants: {len(eqtl_formatted)}")
eqtl_formatted.head()
Formatted eQTL data for ENSG00000177663:
Variants: 4338
| SNP | chr | pos | ref | alt | beta | varbeta | pvalue | |
|---|---|---|---|---|---|---|---|---|
| 0 | 22_16585130_T_C | 22 | 16585130 | T | C | -0.065519 | 0.029920 | 0.706084 |
| 1 | 22_16585144_G_A | 22 | 16585144 | G | A | -0.002678 | 0.004836 | 0.969395 |
| 2 | 22_16585510_C_G | 22 | 16585510 | C | G | 0.031384 | 0.001607 | 0.436520 |
| 3 | 22_16585603_G_A | 22 | 16585603 | G | A | 0.005665 | 0.002312 | 0.906565 |
| 4 | 22_16585810_T_C | 22 | 16585810 | T | C | -0.033120 | 0.002137 | 0.476285 |
Download and Prepare GWAS Summary Statistics#
Now we’ll download GWAS summary statistics from the GWAS Catalog. We’ll use a study of coronary artery disease as an example.
gwas_path = get_gwas_catalog_study_summary_stats("GCST90043957", return_path=True) # TODO
print(f"Downloaded GWAS summary statistics to: {gwas_path}")
[2025-12-30 00:44:49,833] INFO:root: Fetching https://www.ebi.ac.uk/gwas/rest/api/v2/studies/GCST90043957
[2025-12-30 00:44:51,205] INFO:root: Found harmonised file: 34737426-GCST90043957-MONDO_0021661.h.tsv.gz
[2025-12-30 00:44:51,206] INFO:root: Downloading http://ftp.ebi.ac.uk/pub/databases/gwas/summary_statistics/GCST90043001-GCST90044000/GCST90043957/harmonised/34737426-GCST90043957-MONDO_0021661.h.tsv.gz to /Users/larnoldt/cellink_data/GCST90043957_summary_stats.tsv.gz
Downloaded GWAS summary statistics to: /Users/larnoldt/cellink_data/GCST90043957_summary_stats.tsv.gz
gwas_data = pd.read_csv(gwas_path, sep="\t", compression="gzip")
print(f"\nGWAS data shape: {gwas_data.shape}")
print(f"Columns: {gwas_data.columns.tolist()}")
gwas_data.head()
GWAS data shape: (11831294, 25)
Columns: ['hm_variant_id', 'hm_rsid', 'hm_chrom', 'hm_pos', 'hm_other_allele', 'hm_effect_allele', 'hm_beta', 'hm_odds_ratio', 'hm_ci_lower', 'hm_ci_upper', 'hm_effect_allele_frequency', 'hm_code', 'chromosome', 'variant_id', 'base_pair_location', 'effect_allele', 'other_allele', 'n', 'effect_allele_frequency', 'beta', 'standard_error', 'p_value', 'odds_ratio', 'ci_lower', 'ci_upper']
| hm_variant_id | hm_rsid | hm_chrom | hm_pos | hm_other_allele | hm_effect_allele | hm_beta | hm_odds_ratio | hm_ci_lower | hm_ci_upper | ... | effect_allele | other_allele | n | effect_allele_frequency | beta | standard_error | p_value | odds_ratio | ci_lower | ci_upper | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1_69569_T_C | rs2531267 | 1.0 | 69569.0 | T | C | 0.084831 | NaN | NaN | NaN | ... | C | T | 456285 | 0.000151 | 0.084831 | 0.481220 | 0.860071 | NaN | NaN | NaN |
| 1 | 1_758351_A_G | rs12238997 | 1.0 | 758351.0 | A | G | 0.004345 | NaN | NaN | NaN | ... | G | A | 418020 | 0.093649 | 0.004345 | 0.020920 | 0.835477 | NaN | NaN | NaN |
| 2 | 1_782207_G_A | rs144155419 | 1.0 | 782207.0 | G | A | -0.012750 | NaN | NaN | NaN | ... | A | G | 446865 | 0.010507 | -0.012750 | 0.057393 | 0.824200 | NaN | NaN | NaN |
| 3 | 1_787949_A_T | rs189787166 | 1.0 | 787949.0 | A | T | 0.005307 | NaN | NaN | NaN | ... | T | A | 455943 | 0.001320 | 0.005307 | 0.158911 | 0.973358 | NaN | NaN | NaN |
| 4 | 1_794707_T_C | rs148120343 | 1.0 | 794707.0 | T | C | 0.023661 | NaN | NaN | NaN | ... | C | T | 432816 | 0.043963 | 0.023661 | 0.029122 | 0.416506 | NaN | NaN | NaN |
5 rows × 25 columns
Filter GWAS to Chromosome and Region#
For colocalization, we only need GWAS variants that overlap with our eQTL analysis region.
def prepare_gwas_for_coloc(gwas_data, chrom, start, end):
"""
Prepare GWAS data for a specific region for coloc analysis.
"""
gwas_region = gwas_data[
(gwas_data["chromosome"] == chrom)
& (gwas_data["base_pair_location"] >= start)
& (gwas_data["base_pair_location"] <= end)
].copy()
if len(gwas_region) == 0:
return None
gwas_region["SNP"] = (
gwas_region["chromosome"].astype(str)
+ "_"
+ gwas_region["base_pair_location"].astype(str)
+ "_"
+ gwas_region["other_allele"]
+ "_"
+ gwas_region["effect_allele"]
)
gwas_region = gwas_region.rename(
columns={
"chromosome": "chr",
"base_pair_location": "pos",
"p_value": "pvalue",
"beta": "beta",
"standard_error": "se",
"effect_allele": "alt",
"other_allele": "ref",
}
)
gwas_region["varbeta"] = gwas_region["se"] ** 2
return gwas_region[["SNP", "chr", "pos", "ref", "alt", "beta", "varbeta", "pvalue"]]
gene_info = dd.C.var.loc[example_gene]
region_start = max(0, gene_info["start"] - cis_window)
region_end = gene_info["end"] + cis_window
gwas_formatted = prepare_gwas_for_coloc(gwas_data, chrom, region_start, region_end)
print(f"\nGWAS variants in region: {len(gwas_formatted) if gwas_formatted is not None else 0}")
if gwas_formatted is not None:
gwas_formatted.head()
GWAS variants in region: 4237
Harmonize eQTL and GWAS Data#
Before running colocalization, we need to ensure that both datasets share the same set of variants and have alleles aligned in the same direction.
def harmonize_datasets(eqtl_data, gwas_data):
"""
Harmonize eQTL and GWAS datasets for colocalization.
Ensures both datasets contain the same variants with aligned alleles.
"""
merged = eqtl_data.merge(gwas_data, on="SNP", suffixes=("_eqtl", "_gwas"), how="inner")
if len(merged) == 0:
print("Warning: No overlapping variants found!")
return None, None, 0
print(f"Overlapping variants: {len(merged)}")
# Check for allele flips (ref/alt swapped)
same_alleles = (merged["ref_eqtl"] == merged["ref_gwas"]) & (merged["alt_eqtl"] == merged["alt_gwas"])
flipped_alleles = (merged["ref_eqtl"] == merged["alt_gwas"]) & (merged["alt_eqtl"] == merged["ref_gwas"])
valid = same_alleles | flipped_alleles
merged = merged[valid].copy()
n_flipped = flipped_alleles[valid].sum()
print(f"Variants after allele harmonization: {len(merged)}")
print(f"Alleles flipped: {n_flipped}")
merged.loc[flipped_alleles[valid], "beta_gwas"] *= -1
eqtl_harmonized = pd.DataFrame(
{
"SNP": merged["SNP"],
"chr": merged["chr_eqtl"],
"pos": merged["pos_eqtl"],
"beta": merged["beta_eqtl"],
"varbeta": merged["varbeta_eqtl"],
"pvalue": merged["pvalue_eqtl"],
}
)
gwas_harmonized = pd.DataFrame(
{
"SNP": merged["SNP"],
"chr": merged["chr_gwas"],
"pos": merged["pos_gwas"],
"beta": merged["beta_gwas"],
"varbeta": merged["varbeta_gwas"],
"pvalue": merged["pvalue_gwas"],
}
)
return eqtl_harmonized, gwas_harmonized, n_flipped
eqtl_harm, gwas_harm, n_flipped = harmonize_datasets(eqtl_formatted, gwas_formatted)
if eqtl_harm is not None:
print(f"\nReady for colocalization with {len(eqtl_harm)} shared variants")
Overlapping variants: 2338
Variants after allele harmonization: 2338
Alleles flipped: 0
Ready for colocalization with 2338 shared variants
Run Colocalization Analysis with coloc#
Now we’ll run the coloc Bayesian colocalization analysis using R’s coloc package via rpy2.
def run_coloc(eqtl_data, gwas_data, n_samples_eqtl, n_samples_gwas, p1=1e-4, p2=1e-4, p12=1e-5, sdY=1.0):
"""
Run coloc colocalization analysis using R's coloc package.
Parameters
----------
eqtl_data : pd.DataFrame
eQTL summary statistics (beta, varbeta, pvalue, SNP)
gwas_data : pd.DataFrame
GWAS summary statistics (beta, varbeta, pvalue, SNP)
n_samples_eqtl : int
Sample size for eQTL study
n_samples_gwas : int
Sample size for GWAS study
p1 : float
Prior probability a SNP is associated with trait 1
p2 : float
Prior probability a SNP is associated with trait 2
p12 : float
Prior probability a SNP is associated with both traits
sdY : float
Standard deviation of the quantitative trait (eQTL expression)
Default is 1.0 for standardized/normalized expression
Returns
-------
dict
Colocalization results including posterior probabilities
"""
dataset1 = ro.ListVector(
{
"beta": ro.FloatVector(eqtl_data["beta"].values),
"varbeta": ro.FloatVector(eqtl_data["varbeta"].values),
"snp": ro.StrVector(eqtl_data["SNP"].values),
"type": "quant",
"N": n_samples_eqtl,
"sdY": sdY,
}
)
dataset2 = ro.ListVector(
{
"beta": ro.FloatVector(gwas_data["beta"].values),
"varbeta": ro.FloatVector(gwas_data["varbeta"].values),
"snp": ro.StrVector(gwas_data["SNP"].values),
"type": "cc",
"N": n_samples_gwas,
}
)
result = coloc.coloc_abf(dataset1=dataset1, dataset2=dataset2, p1=p1, p2=p2, p12=p12)
summary = result.rx2("summary")
results_dict = {
"nsnps": int(summary[0]),
"PP.H0.abf": float(summary[1]),
"PP.H1.abf": float(summary[2]),
"PP.H2.abf": float(summary[3]),
"PP.H3.abf": float(summary[4]),
"PP.H4.abf": float(summary[5]),
}
return results_dict
if eqtl_harm is not None:
coloc_result = run_coloc(
eqtl_data=eqtl_harm,
gwas_data=gwas_harm,
n_samples_eqtl=dd.shape[0],
n_samples_gwas=456348,
p1=coloc_p1,
p2=coloc_p2,
p12=coloc_p12,
)
print(f"\n{'='*60}")
print(f"Colocalization Results for {example_gene}")
print(f"{'='*60}")
print(f"Number of SNPs: {coloc_result['nsnps']}")
print("\nPosterior Probabilities:")
print(f" PP.H0 (no association): {coloc_result['PP.H0.abf']:.4f}")
print(f" PP.H1 (eQTL only): {coloc_result['PP.H1.abf']:.4f}")
print(f" PP.H2 (GWAS only): {coloc_result['PP.H2.abf']:.4f}")
print(f" PP.H3 (both, different variants): {coloc_result['PP.H3.abf']:.4f}")
print(f" PP.H4 (colocalization): {coloc_result['PP.H4.abf']:.4f}")
print("\nInterpretation: ", end="")
if coloc_result["PP.H4.abf"] > 0.8:
print("Strong evidence for colocalization ✓")
elif coloc_result["PP.H4.abf"] > 0.5:
print("Moderate evidence for colocalization")
elif coloc_result["PP.H3.abf"] > 0.5:
print("Likely independent signals")
else:
print("Inconclusive")
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.30e-06 8.50e-01 1.42e-07 5.22e-02 9.83e-02
[1] "PP abf for shared variant: 9.83%"
============================================================
Colocalization Results for ENSG00000177663
============================================================
Number of SNPs: 2338
Posterior Probabilities:
PP.H0 (no association): 0.0000
PP.H1 (eQTL only): 0.8496
PP.H2 (GWAS only): 0.0000
PP.H3 (both, different variants): 0.0522
PP.H4 (colocalization): 0.0983
Interpretation: Inconclusive
Genome-wide Colocalization Screen#
Now let’s perform colocalization analysis for all eGenes (genes with significant eQTLs).
def screen_colocalizations(eqtl_results, gwas_data, gene_list, dd, chrom, cis_window=500_000, pp_h4_threshold=0.5):
"""
Perform genome-wide colocalization screen.
"""
results = []
for gene_id in gene_list:
try:
if gene_id not in dd.C.var.index:
continue
gene_info = dd.C.var.loc[gene_id]
eqtl_gene = prepare_eqtl_for_coloc(eqtl_results, gene_id)
if eqtl_gene is None or len(eqtl_gene) < 10:
continue
region_start = max(0, gene_info["start"] - cis_window)
region_end = gene_info["end"] + cis_window
gwas_region = prepare_gwas_for_coloc(gwas_data, chrom, region_start, region_end)
if gwas_region is None or len(gwas_region) < 10:
continue
eqtl_harm, gwas_harm, n_flipped = harmonize_datasets(eqtl_gene, gwas_region)
if eqtl_harm is None or len(eqtl_harm) < 10:
continue
coloc_result = run_coloc(
eqtl_data=eqtl_harm, gwas_data=gwas_harm, n_samples_eqtl=dd.shape[0], n_samples_gwas=456348
)
results.append(
{
"gene_id": gene_id,
"gene_name": gene_info.get("gene_name", gene_id),
"chr": chrom,
"start": gene_info["start"],
"end": gene_info["end"],
"n_snps": coloc_result["nsnps"],
"PP.H0": coloc_result["PP.H0.abf"],
"PP.H1": coloc_result["PP.H1.abf"],
"PP.H2": coloc_result["PP.H2.abf"],
"PP.H3": coloc_result["PP.H3.abf"],
"PP.H4": coloc_result["PP.H4.abf"],
}
)
except Exception as e:
print(f"Error processing {gene_id}: {e}")
continue
results_df = pd.DataFrame(results)
if len(results_df) > 0:
results_df = results_df.sort_values("PP.H4", ascending=False)
significant = results_df[results_df["PP.H4"] >= pp_h4_threshold]
print("\nGenome-wide Colocalization Summary:")
print(f" Genes tested: {len(results_df)}")
print(f" PP.H4 >= {pp_h4_threshold}: {len(significant)}")
print(f" PP.H4 >= 0.8 (strong): {(results_df['PP.H4'] >= 0.8).sum()}")
return results_df
genes_with_eqtls = cis_qtl_pairs.groupby("phenotype_id").size()
genes_to_test = genes_with_eqtls[genes_with_eqtls >= 50].index.tolist() # [:20] # Test first 20 for demo #TODO
print(f"Testing {len(genes_to_test)} genes for colocalization...")
coloc_results = screen_colocalizations(
eqtl_results=cis_qtl_pairs,
gwas_data=gwas_data,
gene_list=genes_to_test,
dd=dd,
chrom=chrom,
cis_window=cis_window,
pp_h4_threshold=0.5,
)
Testing 446 genes for colocalization...
Overlapping variants: 2921
Variants after allele harmonization: 2921
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71300 0.19200 0.07000 0.01880 0.00672
[1] "PP abf for shared variant: 0.672%"
Overlapping variants: 2428
Variants after allele harmonization: 2428
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73700 0.18000 0.06120 0.01500 0.00614
[1] "PP abf for shared variant: 0.614%"
Overlapping variants: 2493
Variants after allele harmonization: 2493
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.32e-04 6.94e-01 1.12e-05 5.88e-02 2.47e-01
[1] "PP abf for shared variant: 24.7%"
Overlapping variants: 2632
Variants after allele harmonization: 2632
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.99e-11 8.23e-01 7.60e-12 1.57e-01 1.97e-02
[1] "PP abf for shared variant: 1.97%"
Overlapping variants: 3914
Variants after allele harmonization: 3914
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.64200 0.24800 0.07560 0.02920 0.00558
[1] "PP abf for shared variant: 0.558%"
Overlapping variants: 2477
Variants after allele harmonization: 2477
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01690 0.90600 0.00107 0.05750 0.01850
[1] "PP abf for shared variant: 1.85%"
Overlapping variants: 2765
Variants after allele harmonization: 2765
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3920 0.1060 0.3770 0.1010 0.0232
[1] "PP abf for shared variant: 2.32%"
Overlapping variants: 2199
Variants after allele harmonization: 2199
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.29e-10 5.16e-01 2.11e-10 4.75e-01 9.41e-03
[1] "PP abf for shared variant: 0.941%"
Overlapping variants: 1702
Variants after allele harmonization: 1702
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.29e-34 5.17e-01 1.16e-34 4.69e-01 1.42e-02
[1] "PP abf for shared variant: 1.42%"
Overlapping variants: 3360
Variants after allele harmonization: 3360
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.81800 0.00739 0.17200 0.00155 0.00150
[1] "PP abf for shared variant: 0.15%"
Overlapping variants: 3240
Variants after allele harmonization: 3240
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.67700 0.15100 0.13600 0.03030 0.00611
[1] "PP abf for shared variant: 0.611%"
Overlapping variants: 2956
Variants after allele harmonization: 2956
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.44e-12 8.86e-01 4.92e-13 9.82e-02 1.55e-02
[1] "PP abf for shared variant: 1.55%"
Overlapping variants: 2936
Variants after allele harmonization: 2936
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72500 0.17100 0.08020 0.01890 0.00478
[1] "PP abf for shared variant: 0.478%"
Overlapping variants: 3197
Variants after allele harmonization: 3197
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75000 0.14100 0.08490 0.01600 0.00815
[1] "PP abf for shared variant: 0.815%"
Overlapping variants: 3477
Variants after allele harmonization: 3477
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 2953
Variants after allele harmonization: 2953
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.006400 0.887000 0.000424 0.058700 0.047100
[1] "PP abf for shared variant: 4.71%"
Overlapping variants: 1516
Variants after allele harmonization: 1516
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.14700 0.78800 0.00735 0.03920 0.01840
[1] "PP abf for shared variant: 1.84%"
Overlapping variants: 3363
Variants after allele harmonization: 3363
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.74100 0.15700 0.07920 0.01680 0.00622
[1] "PP abf for shared variant: 0.622%"
Overlapping variants: 2811
Variants after allele harmonization: 2811
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 2738
Variants after allele harmonization: 2738
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4870 0.1230 0.2960 0.0747 0.0199
[1] "PP abf for shared variant: 1.99%"
Overlapping variants: 2681
Variants after allele harmonization: 2681
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76300 0.16800 0.05220 0.01150 0.00479
[1] "PP abf for shared variant: 0.479%"
Overlapping variants: 2783
Variants after allele harmonization: 2783
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.42e-12 6.17e-01 8.43e-13 3.67e-01 1.56e-02
[1] "PP abf for shared variant: 1.56%"
Overlapping variants: 2589
Variants after allele harmonization: 2589
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.65600 0.18600 0.11700 0.03310 0.00802
[1] "PP abf for shared variant: 0.802%"
Overlapping variants: 2616
Variants after allele harmonization: 2616
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.69800 0.14500 0.12400 0.02590 0.00648
[1] "PP abf for shared variant: 0.648%"
Overlapping variants: 2609
Variants after allele harmonization: 2609
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78200 0.06150 0.13900 0.01090 0.00701
[1] "PP abf for shared variant: 0.701%"
Overlapping variants: 2454
Variants after allele harmonization: 2454
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3670 0.4590 0.0708 0.0884 0.0143
[1] "PP abf for shared variant: 1.43%"
Overlapping variants: 2535
Variants after allele harmonization: 2535
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.74100 0.14700 0.08870 0.01760 0.00556
[1] "PP abf for shared variant: 0.556%"
Overlapping variants: 1686
Variants after allele harmonization: 1686
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78400 0.14700 0.05460 0.01020 0.00486
[1] "PP abf for shared variant: 0.486%"
Overlapping variants: 1612
Variants after allele harmonization: 1612
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88800 0.04710 0.06020 0.00319 0.00162
[1] "PP abf for shared variant: 0.162%"
Overlapping variants: 1478
Variants after allele harmonization: 1478
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72100 0.21900 0.03940 0.01200 0.00855
[1] "PP abf for shared variant: 0.855%"
Overlapping variants: 2772
Variants after allele harmonization: 2772
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.03e-09 9.08e-01 1.61e-10 7.22e-02 2.00e-02
[1] "PP abf for shared variant: 2%"
Overlapping variants: 2797
Variants after allele harmonization: 2797
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71000 0.20000 0.06380 0.01800 0.00729
[1] "PP abf for shared variant: 0.729%"
Overlapping variants: 2605
Variants after allele harmonization: 2605
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
8.52e-09 9.03e-01 7.25e-10 7.68e-02 1.99e-02
[1] "PP abf for shared variant: 1.99%"
Overlapping variants: 3288
Variants after allele harmonization: 3288
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72900 0.17000 0.07760 0.01810 0.00604
[1] "PP abf for shared variant: 0.604%"
Overlapping variants: 2357
Variants after allele harmonization: 2357
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 2360
Variants after allele harmonization: 2360
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.69200 0.21600 0.06490 0.02020 0.00774
[1] "PP abf for shared variant: 0.774%"
Overlapping variants: 2269
Variants after allele harmonization: 2269
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
8.10e-05 8.03e-01 1.73e-05 1.71e-01 2.59e-02
[1] "PP abf for shared variant: 2.59%"
Overlapping variants: 2498
Variants after allele harmonization: 2498
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.06200 0.82800 0.00599 0.08000 0.02390
[1] "PP abf for shared variant: 2.39%"
Overlapping variants: 2370
Variants after allele harmonization: 2370
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6810 0.1050 0.1470 0.0226 0.0440
[1] "PP abf for shared variant: 4.4%"
Overlapping variants: 1933
Variants after allele harmonization: 1933
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.62e-04 9.04e-01 1.31e-05 7.30e-02 2.26e-02
[1] "PP abf for shared variant: 2.26%"
Overlapping variants: 2335
Variants after allele harmonization: 2335
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72700 0.09810 0.14800 0.02000 0.00679
[1] "PP abf for shared variant: 0.679%"
Overlapping variants: 2391
Variants after allele harmonization: 2391
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.41e-07 8.11e-01 2.89e-08 1.67e-01 2.25e-02
[1] "PP abf for shared variant: 2.25%"
Overlapping variants: 2351
Variants after allele harmonization: 2351
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01270 0.80000 0.00257 0.16200 0.02300
[1] "PP abf for shared variant: 2.3%"
Overlapping variants: 2519
Variants after allele harmonization: 2519
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.2580 0.6310 0.0284 0.0695 0.0129
[1] "PP abf for shared variant: 1.29%"
Overlapping variants: 1802
Variants after allele harmonization: 1802
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87600 0.08820 0.03050 0.00307 0.00194
[1] "PP abf for shared variant: 0.194%"
Overlapping variants: 2223
Variants after allele harmonization: 2223
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.22e-10 8.84e-01 5.54e-11 9.39e-02 2.23e-02
[1] "PP abf for shared variant: 2.23%"
Overlapping variants: 1937
Variants after allele harmonization: 1937
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.32e-06 9.31e-01 1.63e-07 3.52e-02 3.41e-02
[1] "PP abf for shared variant: 3.41%"
Overlapping variants: 2242
Variants after allele harmonization: 2242
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76200 0.13500 0.08010 0.01420 0.00831
[1] "PP abf for shared variant: 0.831%"
Overlapping variants: 2356
Variants after allele harmonization: 2356
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73200 0.10000 0.14200 0.01950 0.00638
[1] "PP abf for shared variant: 0.638%"
Overlapping variants: 2076
Variants after allele harmonization: 2076
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.53100 0.42600 0.02110 0.01690 0.00481
[1] "PP abf for shared variant: 0.481%"
Overlapping variants: 2287
Variants after allele harmonization: 2287
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.47e-17 8.90e-01 1.54e-18 9.34e-02 1.69e-02
[1] "PP abf for shared variant: 1.69%"
Overlapping variants: 2138
Variants after allele harmonization: 2138
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.79800 0.15900 0.03270 0.00652 0.00305
[1] "PP abf for shared variant: 0.305%"
Overlapping variants: 2358
Variants after allele harmonization: 2358
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76400 0.07260 0.14500 0.01380 0.00439
[1] "PP abf for shared variant: 0.439%"
Overlapping variants: 2168
Variants after allele harmonization: 2168
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5980 0.3330 0.0248 0.0138 0.0307
[1] "PP abf for shared variant: 3.07%"
Overlapping variants: 2571
Variants after allele harmonization: 2571
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73600 0.16700 0.07410 0.01680 0.00628
[1] "PP abf for shared variant: 0.628%"
Overlapping variants: 1812
Variants after allele harmonization: 1812
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4610 0.0561 0.4190 0.0510 0.0130
[1] "PP abf for shared variant: 1.3%"
Overlapping variants: 2214
Variants after allele harmonization: 2214
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6530 0.2520 0.0619 0.0239 0.0101
[1] "PP abf for shared variant: 1.01%"
Overlapping variants: 1913
Variants after allele harmonization: 1913
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.04e-04 5.15e-01 9.49e-05 4.69e-01 1.55e-02
[1] "PP abf for shared variant: 1.55%"
Overlapping variants: 2543
Variants after allele harmonization: 2543
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80000 0.13400 0.05350 0.00894 0.00419
[1] "PP abf for shared variant: 0.419%"
Overlapping variants: 1993
Variants after allele harmonization: 1993
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77200 0.15400 0.05730 0.01140 0.00536
[1] "PP abf for shared variant: 0.536%"
Overlapping variants: 1971
Variants after allele harmonization: 1971
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7390 0.1850 0.0530 0.0133 0.0100
[1] "PP abf for shared variant: 1%"
Overlapping variants: 2684
Variants after allele harmonization: 2684
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4780 0.0375 0.4440 0.0349 0.0055
[1] "PP abf for shared variant: 0.55%"
Overlapping variants: 1969
Variants after allele harmonization: 1969
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77800 0.14900 0.05680 0.01080 0.00546
[1] "PP abf for shared variant: 0.546%"
Overlapping variants: 3287
Variants after allele harmonization: 3287
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
8.05e-10 8.97e-01 6.86e-11 7.65e-02 2.61e-02
[1] "PP abf for shared variant: 2.61%"
Overlapping variants: 2019
Variants after allele harmonization: 2019
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76700 0.15500 0.05970 0.01210 0.00597
[1] "PP abf for shared variant: 0.597%"
Overlapping variants: 2812
Variants after allele harmonization: 2812
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78500 0.14100 0.05880 0.01060 0.00412
[1] "PP abf for shared variant: 0.412%"
Overlapping variants: 2088
Variants after allele harmonization: 2088
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82600 0.12200 0.04280 0.00633 0.00315
[1] "PP abf for shared variant: 0.315%"
Overlapping variants: 2836
Variants after allele harmonization: 2836
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.60e-13 9.07e-01 5.61e-14 6.69e-02 2.63e-02
[1] "PP abf for shared variant: 2.63%"
Overlapping variants: 2100
Variants after allele harmonization: 2100
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.03140 0.89600 0.00166 0.04720 0.02360
[1] "PP abf for shared variant: 2.36%"
Overlapping variants: 2098
Variants after allele harmonization: 2098
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7340 0.2130 0.0386 0.0112 0.0038
[1] "PP abf for shared variant: 0.38%"
Overlapping variants: 2882
Variants after allele harmonization: 2882
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76000 0.16200 0.05670 0.01210 0.00874
[1] "PP abf for shared variant: 0.874%"
Overlapping variants: 1876
Variants after allele harmonization: 1876
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.014700 0.872000 0.000651 0.038500 0.073900
[1] "PP abf for shared variant: 7.39%"
Overlapping variants: 2918
Variants after allele harmonization: 2918
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
9.83e-08 9.02e-01 7.25e-09 6.65e-02 3.10e-02
[1] "PP abf for shared variant: 3.1%"
Overlapping variants: 1855
Variants after allele harmonization: 1855
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.73e-04 9.36e-01 7.61e-06 4.10e-02 2.30e-02
[1] "PP abf for shared variant: 2.3%"
Overlapping variants: 1863
Variants after allele harmonization: 1863
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80300 0.15100 0.03560 0.00670 0.00364
[1] "PP abf for shared variant: 0.364%"
Overlapping variants: 1518
Variants after allele harmonization: 1518
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82600 0.11800 0.04540 0.00645 0.00417
[1] "PP abf for shared variant: 0.417%"
Overlapping variants: 1785
Variants after allele harmonization: 1785
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0714 0.8600 0.0032 0.0385 0.0265
[1] "PP abf for shared variant: 2.65%"
Overlapping variants: 1815
Variants after allele harmonization: 1815
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.83300 0.11500 0.04260 0.00590 0.00344
[1] "PP abf for shared variant: 0.344%"
Overlapping variants: 1550
Variants after allele harmonization: 1550
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88500 0.05400 0.05500 0.00335 0.00246
[1] "PP abf for shared variant: 0.246%"
Overlapping variants: 3526
Variants after allele harmonization: 3526
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77100 0.14400 0.06800 0.01270 0.00421
[1] "PP abf for shared variant: 0.421%"
Overlapping variants: 1596
Variants after allele harmonization: 1596
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.014400 0.925000 0.000646 0.041600 0.018400
[1] "PP abf for shared variant: 1.84%"
Overlapping variants: 3517
Variants after allele harmonization: 3517
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.53900 0.28100 0.11300 0.05910 0.00779
[1] "PP abf for shared variant: 0.779%"
Overlapping variants: 1726
Variants after allele harmonization: 1726
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88600 0.04930 0.05990 0.00334 0.00162
[1] "PP abf for shared variant: 0.162%"
Overlapping variants: 3581
Variants after allele harmonization: 3581
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01110 0.81700 0.00209 0.15500 0.01520
[1] "PP abf for shared variant: 1.52%"
Overlapping variants: 1806
Variants after allele harmonization: 1806
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82000 0.11400 0.05280 0.00735 0.00544
[1] "PP abf for shared variant: 0.544%"
Overlapping variants: 2574
Variants after allele harmonization: 2574
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88200 0.04570 0.06710 0.00347 0.00164
[1] "PP abf for shared variant: 0.164%"
Overlapping variants: 1844
Variants after allele harmonization: 1844
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1470 0.7230 0.0169 0.0831 0.0294
[1] "PP abf for shared variant: 2.94%"
Overlapping variants: 1999
Variants after allele harmonization: 1999
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.006890 0.902000 0.000479 0.062700 0.027900
[1] "PP abf for shared variant: 2.79%"
Overlapping variants: 1891
Variants after allele harmonization: 1891
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.22700 0.70400 0.01470 0.04550 0.00868
[1] "PP abf for shared variant: 0.868%"
Overlapping variants: 1829
Variants after allele harmonization: 1829
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75300 0.13700 0.08640 0.01570 0.00845
[1] "PP abf for shared variant: 0.845%"
Overlapping variants: 3470
Variants after allele harmonization: 3470
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6410 0.1920 0.1210 0.0360 0.0106
[1] "PP abf for shared variant: 1.06%"
Overlapping variants: 1978
Variants after allele harmonization: 1978
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.04090 0.87600 0.00267 0.05710 0.02370
[1] "PP abf for shared variant: 2.37%"
Overlapping variants: 3324
Variants after allele harmonization: 3324
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6840 0.1520 0.1260 0.0280 0.0102
[1] "PP abf for shared variant: 1.02%"
Overlapping variants: 2066
Variants after allele harmonization: 2066
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.001620 0.915000 0.000107 0.060200 0.023100
[1] "PP abf for shared variant: 2.31%"
Overlapping variants: 2584
Variants after allele harmonization: 2584
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77100 0.16800 0.04520 0.00983 0.00608
[1] "PP abf for shared variant: 0.608%"
Overlapping variants: 2945
Variants after allele harmonization: 2945
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3050 0.5240 0.0528 0.0907 0.0267
[1] "PP abf for shared variant: 2.67%"
Overlapping variants: 2615
Variants after allele harmonization: 2615
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.66e-07 8.81e-01 4.67e-08 8.83e-02 3.03e-02
[1] "PP abf for shared variant: 3.03%"
Overlapping variants: 2173
Variants after allele harmonization: 2173
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80300 0.12500 0.05880 0.00915 0.00448
[1] "PP abf for shared variant: 0.448%"
Overlapping variants: 2928
Variants after allele harmonization: 2928
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73500 0.19400 0.05240 0.01380 0.00467
[1] "PP abf for shared variant: 0.467%"
Overlapping variants: 2079
Variants after allele harmonization: 2079
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82100 0.10800 0.05870 0.00772 0.00511
[1] "PP abf for shared variant: 0.511%"
Overlapping variants: 2514
Variants after allele harmonization: 2514
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71500 0.20100 0.06130 0.01720 0.00563
[1] "PP abf for shared variant: 0.563%"
Overlapping variants: 2016
Variants after allele harmonization: 2016
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.60900 0.03900 0.32600 0.02090 0.00564
[1] "PP abf for shared variant: 0.564%"
Overlapping variants: 3330
Variants after allele harmonization: 3330
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.52400 0.39500 0.04260 0.03210 0.00639
[1] "PP abf for shared variant: 0.639%"
Overlapping variants: 3046
Variants after allele harmonization: 3046
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5460 0.3720 0.0406 0.0276 0.0141
[1] "PP abf for shared variant: 1.41%"
Overlapping variants: 1970
Variants after allele harmonization: 1970
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.44e-06 6.37e-01 1.33e-06 3.46e-01 1.75e-02
[1] "PP abf for shared variant: 1.75%"
Overlapping variants: 2068
Variants after allele harmonization: 2068
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5440 0.0946 0.2970 0.0516 0.0128
[1] "PP abf for shared variant: 1.28%"
Overlapping variants: 2323
Variants after allele harmonization: 2323
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.79200 0.11000 0.08100 0.01130 0.00546
[1] "PP abf for shared variant: 0.546%"
Overlapping variants: 2213
Variants after allele harmonization: 2213
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6670 0.2270 0.0667 0.0226 0.0168
[1] "PP abf for shared variant: 1.68%"
Overlapping variants: 1943
Variants after allele harmonization: 1943
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6140 0.0311 0.3330 0.0169 0.0048
[1] "PP abf for shared variant: 0.48%"
Overlapping variants: 2222
Variants after allele harmonization: 2222
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78300 0.13600 0.06260 0.01080 0.00754
[1] "PP abf for shared variant: 0.754%"
Overlapping variants: 3027
Variants after allele harmonization: 3027
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8700 0.0000 0.0635 0.0661
[1] "PP abf for shared variant: 6.61%"
Overlapping variants: 2068
Variants after allele harmonization: 2068
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75800 0.14900 0.07220 0.01420 0.00688
[1] "PP abf for shared variant: 0.688%"
Overlapping variants: 3008
Variants after allele harmonization: 3008
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80500 0.12300 0.05870 0.00898 0.00386
[1] "PP abf for shared variant: 0.386%"
Overlapping variants: 1996
Variants after allele harmonization: 1996
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5740 0.0649 0.3130 0.0354 0.0122
[1] "PP abf for shared variant: 1.22%"
Overlapping variants: 2078
Variants after allele harmonization: 2078
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80900 0.09860 0.07770 0.00947 0.00514
[1] "PP abf for shared variant: 0.514%"
Overlapping variants: 2080
Variants after allele harmonization: 2080
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.42e-50 7.59e-01 9.83e-52 5.25e-02 1.88e-01
[1] "PP abf for shared variant: 18.8%"
Overlapping variants: 2024
Variants after allele harmonization: 2024
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76900 0.15500 0.05950 0.01200 0.00488
[1] "PP abf for shared variant: 0.488%"
Overlapping variants: 2999
Variants after allele harmonization: 2999
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71200 0.21600 0.05160 0.01570 0.00516
[1] "PP abf for shared variant: 0.516%"
Overlapping variants: 3002
Variants after allele harmonization: 3002
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1560 0.7510 0.0113 0.0544 0.0265
[1] "PP abf for shared variant: 2.65%"
Overlapping variants: 2119
Variants after allele harmonization: 2119
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77000 0.15900 0.05350 0.01100 0.00698
[1] "PP abf for shared variant: 0.698%"
Overlapping variants: 1909
Variants after allele harmonization: 1909
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75400 0.14400 0.07860 0.01500 0.00786
[1] "PP abf for shared variant: 0.786%"
Overlapping variants: 1963
Variants after allele harmonization: 1963
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5480 0.1020 0.2810 0.0525 0.0163
[1] "PP abf for shared variant: 1.63%"
Overlapping variants: 1873
Variants after allele harmonization: 1873
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4130 0.4390 0.0474 0.0504 0.0502
[1] "PP abf for shared variant: 5.02%"
Overlapping variants: 1881
Variants after allele harmonization: 1881
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.001310 0.879000 0.000151 0.101000 0.018900
[1] "PP abf for shared variant: 1.89%"
Overlapping variants: 1950
Variants after allele harmonization: 1950
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5410 0.0791 0.3170 0.0463 0.0174
[1] "PP abf for shared variant: 1.74%"
Overlapping variants: 2368
Variants after allele harmonization: 2368
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
8.34e-08 6.02e-01 5.31e-08 3.83e-01 1.44e-02
[1] "PP abf for shared variant: 1.44%"
Overlapping variants: 1799
Variants after allele harmonization: 1799
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.68700 0.20300 0.07900 0.02340 0.00733
[1] "PP abf for shared variant: 0.733%"
Overlapping variants: 2147
Variants after allele harmonization: 2147
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4870 0.4330 0.0326 0.0290 0.0181
[1] "PP abf for shared variant: 1.81%"
Overlapping variants: 2091
Variants after allele harmonization: 2091
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.17900 0.74800 0.01240 0.05180 0.00844
[1] "PP abf for shared variant: 0.844%"
Overlapping variants: 2310
Variants after allele harmonization: 2310
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78600 0.14300 0.05680 0.01030 0.00449
[1] "PP abf for shared variant: 0.449%"
Overlapping variants: 1882
Variants after allele harmonization: 1882
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
9.48e-23 7.43e-01 3.02e-23 2.37e-01 2.06e-02
[1] "PP abf for shared variant: 2.06%"
Overlapping variants: 3090
Variants after allele harmonization: 3090
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76500 0.14700 0.06980 0.01340 0.00461
[1] "PP abf for shared variant: 0.461%"
Overlapping variants: 2421
Variants after allele harmonization: 2421
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71500 0.20700 0.05590 0.01620 0.00567
[1] "PP abf for shared variant: 0.567%"
Overlapping variants: 2506
Variants after allele harmonization: 2506
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.011900 0.898000 0.000953 0.071800 0.017000
[1] "PP abf for shared variant: 1.7%"
Overlapping variants: 1267
Variants after allele harmonization: 1267
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.001150 0.650000 0.000564 0.319000 0.029600
[1] "PP abf for shared variant: 2.96%"
Overlapping variants: 2572
Variants after allele harmonization: 2572
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.68000 0.23500 0.05830 0.02010 0.00619
[1] "PP abf for shared variant: 0.619%"
Overlapping variants: 1721
Variants after allele harmonization: 1721
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5180 0.0773 0.3150 0.0469 0.0423
[1] "PP abf for shared variant: 4.23%"
Overlapping variants: 1339
Variants after allele harmonization: 1339
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.61100 0.03200 0.33300 0.01750 0.00613
[1] "PP abf for shared variant: 0.613%"
Overlapping variants: 2537
Variants after allele harmonization: 2537
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73500 0.15900 0.08190 0.01770 0.00651
[1] "PP abf for shared variant: 0.651%"
Overlapping variants: 3296
Variants after allele harmonization: 3296
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6960 0.1840 0.0773 0.0205 0.0221
[1] "PP abf for shared variant: 2.21%"
Overlapping variants: 2664
Variants after allele harmonization: 2664
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.70600 0.18700 0.07930 0.02100 0.00726
[1] "PP abf for shared variant: 0.726%"
Overlapping variants: 2706
Variants after allele harmonization: 2706
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.2250 0.6630 0.0253 0.0744 0.0125
[1] "PP abf for shared variant: 1.25%"
Overlapping variants: 1479
Variants after allele harmonization: 1479
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75500 0.02650 0.20900 0.00731 0.00214
[1] "PP abf for shared variant: 0.214%"
Overlapping variants: 2999
Variants after allele harmonization: 2999
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.00e-04 8.92e-01 2.09e-05 9.35e-02 1.44e-02
[1] "PP abf for shared variant: 1.44%"
Overlapping variants: 2928
Variants after allele harmonization: 2928
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.59e-04 8.99e-01 4.67e-05 9.14e-02 8.70e-03
[1] "PP abf for shared variant: 0.87%"
Overlapping variants: 2515
Variants after allele harmonization: 2515
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7430 0.1490 0.0840 0.0169 0.0066
[1] "PP abf for shared variant: 0.66%"
Overlapping variants: 1460
Variants after allele harmonization: 1460
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6950 0.0927 0.1740 0.0232 0.0144
[1] "PP abf for shared variant: 1.44%"
Overlapping variants: 2576
Variants after allele harmonization: 2576
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.02190 0.83800 0.00244 0.09350 0.04380
[1] "PP abf for shared variant: 4.38%"
Overlapping variants: 1387
Variants after allele harmonization: 1387
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7660 0.0976 0.1120 0.0142 0.0110
[1] "PP abf for shared variant: 1.1%"
Overlapping variants: 1418
Variants after allele harmonization: 1418
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78800 0.11100 0.08460 0.01190 0.00417
[1] "PP abf for shared variant: 0.417%"
Overlapping variants: 1275
Variants after allele harmonization: 1275
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88400 0.03490 0.07640 0.00302 0.00204
[1] "PP abf for shared variant: 0.204%"
Overlapping variants: 1177
Variants after allele harmonization: 1177
Alleles flipped: 0
[2025-12-30 00:50:30,132] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:50:30,132] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:50:30,133] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())
[2025-12-30 00:50:30,133] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]:
Error processing ENSG00000100399: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 1171
Variants after allele harmonization: 1171
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004630 0.931000 0.000222 0.044700 0.019700
[1] "PP abf for shared variant: 1.97%"
Overlapping variants: 1245
Variants after allele harmonization: 1245
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5020 0.4360 0.0246 0.0213 0.0162
[1] "PP abf for shared variant: 1.62%"
Overlapping variants: 1417
Variants after allele harmonization: 1417
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87900 0.06990 0.04430 0.00352 0.00353
[1] "PP abf for shared variant: 0.353%"
Overlapping variants: 1528
Variants after allele harmonization: 1528
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80800 0.13900 0.04210 0.00722 0.00424
[1] "PP abf for shared variant: 0.424%"
Overlapping variants: 1434
Variants after allele harmonization: 1434
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.86e-05 9.35e-01 3.92e-06 4.66e-02 1.84e-02
[1] "PP abf for shared variant: 1.84%"
Overlapping variants: 2973
Variants after allele harmonization: 2973
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75000 0.14700 0.08310 0.01620 0.00409
[1] "PP abf for shared variant: 0.409%"
Overlapping variants: 1375
Variants after allele harmonization: 1375
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.81400 0.13500 0.04020 0.00668 0.00334
[1] "PP abf for shared variant: 0.334%"
Overlapping variants: 1432
Variants after allele harmonization: 1432
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87400 0.07470 0.04410 0.00377 0.00312
[1] "PP abf for shared variant: 0.312%"
Overlapping variants: 3111
Variants after allele harmonization: 3111
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1740 0.6800 0.0192 0.0749 0.0519
[1] "PP abf for shared variant: 5.19%"
Overlapping variants: 3444
Variants after allele harmonization: 3444
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3150 0.5020 0.0636 0.1010 0.0177
[1] "PP abf for shared variant: 1.77%"
Overlapping variants: 3345
Variants after allele harmonization: 3345
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.02740 0.78200 0.00532 0.15200 0.03300
[1] "PP abf for shared variant: 3.3%"
Overlapping variants: 3156
Variants after allele harmonization: 3156
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.003050 0.815000 0.000591 0.158000 0.023200
[1] "PP abf for shared variant: 2.32%"
Overlapping variants: 3168
Variants after allele harmonization: 3168
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.62400 0.20500 0.12200 0.04000 0.00901
[1] "PP abf for shared variant: 0.901%"
Overlapping variants: 3255
Variants after allele harmonization: 3255
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.37e-05 6.43e-01 4.76e-06 1.29e-01 2.29e-01
[1] "PP abf for shared variant: 22.9%"
Overlapping variants: 2546
Variants after allele harmonization: 2546
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71400 0.12200 0.13400 0.02290 0.00707
[1] "PP abf for shared variant: 0.707%"
Overlapping variants: 2712
Variants after allele harmonization: 2712
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01630 0.79600 0.00317 0.15500 0.02910
[1] "PP abf for shared variant: 2.91%"
Overlapping variants: 2718
Variants after allele harmonization: 2718
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.95e-25 9.16e-01 2.85e-26 6.60e-02 1.82e-02
[1] "PP abf for shared variant: 1.82%"
Overlapping variants: 2734
Variants after allele harmonization: 2734
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01590 0.89400 0.00118 0.06620 0.02260
[1] "PP abf for shared variant: 2.26%"
Overlapping variants: 1470
Variants after allele harmonization: 1470
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.86000 0.10800 0.02610 0.00327 0.00243
[1] "PP abf for shared variant: 0.243%"
Overlapping variants: 3435
Variants after allele harmonization: 3435
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.64400 0.27100 0.05540 0.02330 0.00604
[1] "PP abf for shared variant: 0.604%"
Overlapping variants: 3432
Variants after allele harmonization: 3432
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.83e-40 8.95e-01 3.30e-41 7.72e-02 2.80e-02
[1] "PP abf for shared variant: 2.8%"
Overlapping variants: 2201
Variants after allele harmonization: 2201
Alleles flipped: 0
[2025-12-30 00:50:32,916] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:50:32,917] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:50:32,917] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Es gab 33 Warnungen (Anzeige mit warnings())
[2025-12-30 00:50:32,917] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]:
Error processing ENSG00000128266: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 1809
Variants after allele harmonization: 1809
Alleles flipped: 0
[2025-12-30 00:50:33,026] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Error processing ENSG00000128268: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 2135
Variants after allele harmonization: 2135
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.71800 0.18000 0.07530 0.01890 0.00683
[1] "PP abf for shared variant: 0.683%"
Overlapping variants: 1757
Variants after allele harmonization: 1757
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76500 0.12000 0.09300 0.01450 0.00786
[1] "PP abf for shared variant: 0.786%"
Overlapping variants: 2756
Variants after allele harmonization: 2756
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.9070 0.0000 0.0592 0.0333
[1] "PP abf for shared variant: 3.33%"
Overlapping variants: 2232
Variants after allele harmonization: 2232
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5000 0.4170 0.0386 0.0322 0.0128
[1] "PP abf for shared variant: 1.28%"
Overlapping variants: 3055
Variants after allele harmonization: 3055
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72400 0.19800 0.05630 0.01540 0.00535
[1] "PP abf for shared variant: 0.535%"
Overlapping variants: 2570
Variants after allele harmonization: 2570
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0186 0.8640 0.0021 0.0975 0.0181
[1] "PP abf for shared variant: 1.81%"
Overlapping variants: 2547
Variants after allele harmonization: 2547
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.85800 0.04030 0.09610 0.00451 0.00125
[1] "PP abf for shared variant: 0.125%"
Overlapping variants: 2684
Variants after allele harmonization: 2684
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.69e-06 9.11e-01 4.64e-07 7.43e-02 1.45e-02
[1] "PP abf for shared variant: 1.45%"
Overlapping variants: 2124
Variants after allele harmonization: 2124
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4670 0.4510 0.0326 0.0315 0.0178
[1] "PP abf for shared variant: 1.78%"
Overlapping variants: 2538
Variants after allele harmonization: 2538
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72100 0.18100 0.07280 0.01830 0.00726
[1] "PP abf for shared variant: 0.726%"
Overlapping variants: 2037
Variants after allele harmonization: 2037
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77100 0.15500 0.05690 0.01150 0.00563
[1] "PP abf for shared variant: 0.563%"
Overlapping variants: 2085
Variants after allele harmonization: 2085
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6290 0.2680 0.0453 0.0193 0.0385
[1] "PP abf for shared variant: 3.85%"
Overlapping variants: 2384
Variants after allele harmonization: 2384
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.68800 0.22900 0.05670 0.01890 0.00684
[1] "PP abf for shared variant: 0.684%"
Overlapping variants: 3066
Variants after allele harmonization: 3066
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73500 0.17300 0.06910 0.01630 0.00609
[1] "PP abf for shared variant: 0.609%"
Overlapping variants: 3216
Variants after allele harmonization: 3216
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5140 0.3740 0.0538 0.0392 0.0190
[1] "PP abf for shared variant: 1.9%"
Overlapping variants: 2213
Variants after allele harmonization: 2213
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82600 0.09430 0.06890 0.00786 0.00330
[1] "PP abf for shared variant: 0.33%"
Overlapping variants: 2655
Variants after allele harmonization: 2655
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3780 0.5150 0.0357 0.0486 0.0230
[1] "PP abf for shared variant: 2.3%"
Overlapping variants: 2502
Variants after allele harmonization: 2502
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.05690 0.82600 0.00591 0.08580 0.02550
[1] "PP abf for shared variant: 2.55%"
Overlapping variants: 2175
Variants after allele harmonization: 2175
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.81000 0.09130 0.08420 0.00948 0.00531
[1] "PP abf for shared variant: 0.531%"
Overlapping variants: 2139
Variants after allele harmonization: 2139
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.79700 0.14500 0.04530 0.00824 0.00471
[1] "PP abf for shared variant: 0.471%"
Overlapping variants: 3353
Variants after allele harmonization: 3353
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.69300 0.21200 0.06800 0.02080 0.00625
[1] "PP abf for shared variant: 0.625%"
Overlapping variants: 2673
Variants after allele harmonization: 2673
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6280 0.2860 0.0519 0.0236 0.0102
[1] "PP abf for shared variant: 1.02%"
Overlapping variants: 1852
Variants after allele harmonization: 1852
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.83900 0.05480 0.09670 0.00631 0.00294
[1] "PP abf for shared variant: 0.294%"
Overlapping variants: 1696
Variants after allele harmonization: 1696
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.90400 0.03250 0.06010 0.00216 0.00129
[1] "PP abf for shared variant: 0.129%"
Overlapping variants: 1353
Variants after allele harmonization: 1353
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80400 0.16300 0.02350 0.00477 0.00396
[1] "PP abf for shared variant: 0.396%"
Overlapping variants: 1416
Variants after allele harmonization: 1416
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 2280
Variants after allele harmonization: 2280
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.30e-10 8.93e-01 2.23e-11 8.65e-02 2.08e-02
[1] "PP abf for shared variant: 2.08%"
Overlapping variants: 2327
Variants after allele harmonization: 2327
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4500 0.3800 0.0847 0.0715 0.0139
[1] "PP abf for shared variant: 1.39%"
Overlapping variants: 1264
Variants after allele harmonization: 1264
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.2980 0.6270 0.0143 0.0300 0.0312
[1] "PP abf for shared variant: 3.12%"
Overlapping variants: 1669
Variants after allele harmonization: 1669
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87400 0.06330 0.05620 0.00406 0.00217
[1] "PP abf for shared variant: 0.217%"
Overlapping variants: 2773
Variants after allele harmonization: 2773
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.57e-05 8.65e-01 3.45e-06 1.16e-01 1.88e-02
[1] "PP abf for shared variant: 1.88%"
Overlapping variants: 2738
Variants after allele harmonization: 2738
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.41e-09 9.03e-01 2.57e-10 6.80e-02 2.89e-02
[1] "PP abf for shared variant: 2.89%"
Overlapping variants: 1262
Variants after allele harmonization: 1262
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.01e-03 9.53e-01 2.92e-05 2.74e-02 1.82e-02
[1] "PP abf for shared variant: 1.82%"
Overlapping variants: 3231
Variants after allele harmonization: 3231
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6690 0.1540 0.1350 0.0310 0.0115
[1] "PP abf for shared variant: 1.15%"
Overlapping variants: 1382
Variants after allele harmonization: 1382
Alleles flipped: 0
[2025-12-30 00:50:37,417] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:50:37,417] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:50:37,417] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())
[2025-12-30 00:50:37,418] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]:
Error processing ENSG00000172346: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 1769
Variants after allele harmonization: 1769
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.07e-103 8.94e-01 4.61e-104 5.83e-02 4.74e-02
[1] "PP abf for shared variant: 4.74%"
Overlapping variants: 2338
Variants after allele harmonization: 2338
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.30e-06 8.50e-01 1.42e-07 5.22e-02 9.83e-02
[1] "PP abf for shared variant: 9.83%"
Overlapping variants: 2415
Variants after allele harmonization: 2415
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7200 0.1990 0.0596 0.0164 0.0057
[1] "PP abf for shared variant: 0.57%"
Overlapping variants: 1958
Variants after allele harmonization: 1958
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.90e-04 7.56e-01 7.67e-05 1.49e-01 9.49e-02
[1] "PP abf for shared variant: 9.49%"
Overlapping variants: 2224
Variants after allele harmonization: 2224
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.43e-11 8.58e-01 4.59e-12 8.89e-02 5.28e-02
[1] "PP abf for shared variant: 5.28%"
Overlapping variants: 2203
Variants after allele harmonization: 2203
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004500 0.878000 0.000475 0.092700 0.024700
[1] "PP abf for shared variant: 2.47%"
Overlapping variants: 2030
Variants after allele harmonization: 2030
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.907000 0.023200 0.066600 0.001710 0.000905
[1] "PP abf for shared variant: 0.0905%"
Overlapping variants: 2525
Variants after allele harmonization: 2525
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.70e-04 8.72e-01 4.53e-05 1.07e-01 2.08e-02
[1] "PP abf for shared variant: 2.08%"
Overlapping variants: 2285
Variants after allele harmonization: 2285
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.11e-06 9.17e-01 1.36e-07 5.89e-02 2.37e-02
[1] "PP abf for shared variant: 2.37%"
Overlapping variants: 2677
Variants after allele harmonization: 2677
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004890 0.879000 0.000537 0.096500 0.018900
[1] "PP abf for shared variant: 1.89%"
Overlapping variants: 2178
Variants after allele harmonization: 2178
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.77000 0.17500 0.04220 0.00959 0.00283
[1] "PP abf for shared variant: 0.283%"
Overlapping variants: 3189
Variants after allele harmonization: 3189
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004100 0.821000 0.000773 0.155000 0.019500
[1] "PP abf for shared variant: 1.95%"
Overlapping variants: 3145
Variants after allele harmonization: 3145
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.96e-13 8.97e-01 2.88e-14 8.70e-02 1.64e-02
[1] "PP abf for shared variant: 1.64%"
Overlapping variants: 2059
Variants after allele harmonization: 2059
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5450 0.0921 0.2920 0.0494 0.0213
[1] "PP abf for shared variant: 2.13%"
Overlapping variants: 1839
Variants after allele harmonization: 1839
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004460 0.909000 0.000309 0.062900 0.023400
[1] "PP abf for shared variant: 2.34%"
Overlapping variants: 1777
Variants after allele harmonization: 1777
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.68300 0.25000 0.04470 0.01640 0.00537
[1] "PP abf for shared variant: 0.537%"
Overlapping variants: 2362
Variants after allele harmonization: 2362
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0374 0.8870 0.0023 0.0546 0.0186
[1] "PP abf for shared variant: 1.86%"
Overlapping variants: 2709
Variants after allele harmonization: 2709
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6420 0.2850 0.0434 0.0193 0.0103
[1] "PP abf for shared variant: 1.03%"
Overlapping variants: 2777
Variants after allele harmonization: 2777
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3620 0.2870 0.1880 0.1490 0.0138
[1] "PP abf for shared variant: 1.38%"
Overlapping variants: 1153
Variants after allele harmonization: 1153
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1030 0.6140 0.0353 0.2100 0.0369
[1] "PP abf for shared variant: 3.69%"
Overlapping variants: 2164
Variants after allele harmonization: 2164
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78200 0.14200 0.06040 0.01090 0.00465
[1] "PP abf for shared variant: 0.465%"
Overlapping variants: 2142
Variants after allele harmonization: 2142
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.00986 0.64600 0.00496 0.32500 0.01450
[1] "PP abf for shared variant: 1.45%"
Overlapping variants: 1872
Variants after allele harmonization: 1872
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01570 0.86100 0.00185 0.10200 0.01980
[1] "PP abf for shared variant: 1.98%"
Overlapping variants: 1508
Variants after allele harmonization: 1508
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73700 0.05160 0.04850 0.00323 0.16000
[1] "PP abf for shared variant: 16%"
Overlapping variants: 1777
Variants after allele harmonization: 1777
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.50e-16 8.97e-01 3.09e-17 6.15e-02 4.12e-02
[1] "PP abf for shared variant: 4.12%"
Overlapping variants: 1361
Variants after allele harmonization: 1361
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.56200 0.38200 0.02770 0.01880 0.00953
[1] "PP abf for shared variant: 0.953%"
Overlapping variants: 2160
Variants after allele harmonization: 2160
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.007140 0.912000 0.000414 0.052900 0.027400
[1] "PP abf for shared variant: 2.74%"
Overlapping variants: 1506
Variants after allele harmonization: 1506
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.04710 0.87300 0.00288 0.05330 0.02350
[1] "PP abf for shared variant: 2.35%"
Overlapping variants: 1882
Variants after allele harmonization: 1882
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5440 0.1020 0.2780 0.0522 0.0233
[1] "PP abf for shared variant: 2.33%"
Overlapping variants: 2732
Variants after allele harmonization: 2732
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.4480 0.0000 0.4610 0.0907
[1] "PP abf for shared variant: 9.07%"
Overlapping variants: 1929
Variants after allele harmonization: 1929
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.66e-06 6.47e-01 1.33e-06 3.24e-01 2.89e-02
[1] "PP abf for shared variant: 2.89%"
Overlapping variants: 3143
Variants after allele harmonization: 3143
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6310 0.2010 0.1180 0.0377 0.0119
[1] "PP abf for shared variant: 1.19%"
Overlapping variants: 1843
Variants after allele harmonization: 1843
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.015200 0.914000 0.000853 0.051100 0.019300
[1] "PP abf for shared variant: 1.93%"
Overlapping variants: 1456
Variants after allele harmonization: 1456
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.85300 0.09200 0.04640 0.00500 0.00309
[1] "PP abf for shared variant: 0.309%"
Overlapping variants: 2804
Variants after allele harmonization: 2804
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4220 0.0770 0.3870 0.0707 0.0431
[1] "PP abf for shared variant: 4.31%"
Overlapping variants: 2345
Variants after allele harmonization: 2345
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.41200 0.52700 0.02240 0.02860 0.00988
[1] "PP abf for shared variant: 0.988%"
Overlapping variants: 2602
Variants after allele harmonization: 2602
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.45e-56 8.08e-01 1.07e-56 1.59e-01 3.36e-02
[1] "PP abf for shared variant: 3.36%"
Overlapping variants: 2112
Variants after allele harmonization: 2112
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.000 0.891 0.000 0.064 0.045
[1] "PP abf for shared variant: 4.5%"
Overlapping variants: 1613
Variants after allele harmonization: 1613
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.89700 0.03940 0.05950 0.00261 0.00158
[1] "PP abf for shared variant: 0.158%"
Overlapping variants: 1793
Variants after allele harmonization: 1793
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80700 0.12700 0.05310 0.00837 0.00473
[1] "PP abf for shared variant: 0.473%"
Overlapping variants: 1659
Variants after allele harmonization: 1659
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0232 0.9060 0.0012 0.0470 0.0225
[1] "PP abf for shared variant: 2.25%"
Overlapping variants: 2531
Variants after allele harmonization: 2531
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78000 0.05620 0.15000 0.01080 0.00261
[1] "PP abf for shared variant: 0.261%"
Overlapping variants: 2346
Variants after allele harmonization: 2346
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01780 0.80700 0.00337 0.15300 0.01900
[1] "PP abf for shared variant: 1.9%"
Overlapping variants: 1983
Variants after allele harmonization: 1983
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.53700 0.10600 0.29100 0.05740 0.00879
[1] "PP abf for shared variant: 0.879%"
Overlapping variants: 2648
Variants after allele harmonization: 2648
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4140 0.0811 0.3840 0.0753 0.0457
[1] "PP abf for shared variant: 4.57%"
Overlapping variants: 1478
Variants after allele harmonization: 1478
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82100 0.14400 0.02690 0.00471 0.00366
[1] "PP abf for shared variant: 0.366%"
Overlapping variants: 4770
Variants after allele harmonization: 4770
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.09e-08 7.88e-01 1.20e-08 1.86e-01 2.67e-02
[1] "PP abf for shared variant: 2.67%"
Overlapping variants: 2508
Variants after allele harmonization: 2508
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82000 0.12300 0.04660 0.00700 0.00306
[1] "PP abf for shared variant: 0.306%"
Overlapping variants: 2796
Variants after allele harmonization: 2796
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.21600 0.26900 0.22500 0.28100 0.00932
[1] "PP abf for shared variant: 0.932%"
Overlapping variants: 2055
Variants after allele harmonization: 2055
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.54800 0.11100 0.27800 0.05650 0.00615
[1] "PP abf for shared variant: 0.615%"
Overlapping variants: 3822
Variants after allele harmonization: 3822
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.62900 0.25500 0.07750 0.03130 0.00771
[1] "PP abf for shared variant: 0.771%"
Overlapping variants: 2655
Variants after allele harmonization: 2655
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3870 0.5190 0.0333 0.0447 0.0157
[1] "PP abf for shared variant: 1.57%"
Overlapping variants: 3011
Variants after allele harmonization: 3011
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.86e-41 8.69e-01 2.14e-42 1.00e-01 3.10e-02
[1] "PP abf for shared variant: 3.1%"
Overlapping variants: 2125
Variants after allele harmonization: 2125
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.02e-16 3.11e-01 5.49e-17 1.68e-01 5.21e-01
[1] "PP abf for shared variant: 52.1%"
Overlapping variants: 1762
Variants after allele harmonization: 1762
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78500 0.09120 0.10400 0.01210 0.00727
[1] "PP abf for shared variant: 0.727%"
Overlapping variants: 2763
Variants after allele harmonization: 2763
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.2160 0.6860 0.0183 0.0580 0.0220
[1] "PP abf for shared variant: 2.2%"
Overlapping variants: 2351
Variants after allele harmonization: 2351
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5990 0.2230 0.1240 0.0461 0.0083
[1] "PP abf for shared variant: 0.83%"
Overlapping variants: 1382
Variants after allele harmonization: 1382
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.919000 0.012800 0.048800 0.000662 0.018400
[1] "PP abf for shared variant: 1.84%"
Overlapping variants: 2867
Variants after allele harmonization: 2867
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.892000 0.006300 0.101000 0.000714 0.000392
[1] "PP abf for shared variant: 0.0392%"
Overlapping variants: 4491
Variants after allele harmonization: 4491
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.62e-04 7.93e-01 5.43e-05 1.64e-01 4.29e-02
[1] "PP abf for shared variant: 4.29%"
Overlapping variants: 3620
Variants after allele harmonization: 3620
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.54e-14 8.51e-01 3.51e-15 1.17e-01 3.16e-02
[1] "PP abf for shared variant: 3.16%"
Overlapping variants: 3549
Variants after allele harmonization: 3549
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.03740 0.85700 0.00385 0.08810 0.01390
[1] "PP abf for shared variant: 1.39%"
Overlapping variants: 1867
Variants after allele harmonization: 1867
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87700 0.07860 0.03870 0.00346 0.00235
[1] "PP abf for shared variant: 0.235%"
Overlapping variants: 2678
Variants after allele harmonization: 2678
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.9040 0.0000 0.0740 0.0217
[1] "PP abf for shared variant: 2.17%"
Overlapping variants: 2340
Variants after allele harmonization: 2340
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75200 0.19000 0.04090 0.01030 0.00748
[1] "PP abf for shared variant: 0.748%"
Overlapping variants: 1493
Variants after allele harmonization: 1493
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80000 0.02800 0.16400 0.00573 0.00292
[1] "PP abf for shared variant: 0.292%"
Overlapping variants: 1523
Variants after allele harmonization: 1523
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.64500 0.29600 0.03470 0.01590 0.00828
[1] "PP abf for shared variant: 0.828%"
Overlapping variants: 3128
Variants after allele harmonization: 3128
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5030 0.3300 0.0948 0.0622 0.0101
[1] "PP abf for shared variant: 1.01%"
Overlapping variants: 1596
Variants after allele harmonization: 1596
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.2230 0.3990 0.1210 0.2170 0.0401
[1] "PP abf for shared variant: 4.01%"
Overlapping variants: 2529
Variants after allele harmonization: 2529
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.81e-62 8.95e-01 2.24e-63 7.11e-02 3.42e-02
[1] "PP abf for shared variant: 3.42%"
Overlapping variants: 2875
Variants after allele harmonization: 2875
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.46e-10 8.75e-01 5.04e-11 9.88e-02 2.61e-02
[1] "PP abf for shared variant: 2.61%"
Overlapping variants: 2625
Variants after allele harmonization: 2625
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80500 0.13600 0.04790 0.00808 0.00342
[1] "PP abf for shared variant: 0.342%"
Overlapping variants: 3102
Variants after allele harmonization: 3102
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6380 0.1960 0.1200 0.0367 0.0100
[1] "PP abf for shared variant: 1%"
Overlapping variants: 1714
Variants after allele harmonization: 1714
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.61e-10 9.11e-01 9.37e-12 5.29e-02 3.65e-02
[1] "PP abf for shared variant: 3.65%"
Overlapping variants: 2104
Variants after allele harmonization: 2104
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.76400 0.17900 0.04280 0.01000 0.00407
[1] "PP abf for shared variant: 0.407%"
Overlapping variants: 1739
Variants after allele harmonization: 1739
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78200 0.15100 0.05250 0.01010 0.00457
[1] "PP abf for shared variant: 0.457%"
Overlapping variants: 1765
Variants after allele harmonization: 1765
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.83100 0.10200 0.05580 0.00684 0.00419
[1] "PP abf for shared variant: 0.419%"
Overlapping variants: 2781
Variants after allele harmonization: 2781
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.13e-19 4.84e-01 7.42e-19 5.03e-01 1.25e-02
[1] "PP abf for shared variant: 1.25%"
Overlapping variants: 2205
Variants after allele harmonization: 2205
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.78900 0.13300 0.06280 0.01060 0.00467
[1] "PP abf for shared variant: 0.467%"
Overlapping variants: 2281
Variants after allele harmonization: 2281
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.57e-10 9.10e-01 2.08e-11 7.35e-02 1.62e-02
[1] "PP abf for shared variant: 1.62%"
Overlapping variants: 3028
Variants after allele harmonization: 3028
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.46200 0.37600 0.08470 0.06880 0.00897
[1] "PP abf for shared variant: 0.897%"
Overlapping variants: 2919
Variants after allele harmonization: 2919
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6270 0.2650 0.0685 0.0289 0.0109
[1] "PP abf for shared variant: 1.09%"
Overlapping variants: 3490
Variants after allele harmonization: 3490
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.12e-12 8.26e-01 7.73e-13 1.55e-01 1.84e-02
[1] "PP abf for shared variant: 1.84%"
Overlapping variants: 2886
Variants after allele harmonization: 2886
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.45e-12 9.09e-01 5.34e-13 6.51e-02 2.62e-02
[1] "PP abf for shared variant: 2.62%"
Overlapping variants: 1264
Variants after allele harmonization: 1264
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.006800 0.907000 0.000188 0.024900 0.061100
[1] "PP abf for shared variant: 6.11%"
Overlapping variants: 2151
Variants after allele harmonization: 2151
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.93500 0.02380 0.03980 0.00101 0.00053
[1] "PP abf for shared variant: 0.053%"
Overlapping variants: 1752
Variants after allele harmonization: 1752
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.947000 0.018100 0.034400 0.000657 0.000330
[1] "PP abf for shared variant: 0.033%"
Overlapping variants: 1738
Variants after allele harmonization: 1738
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
9.62e-11 9.40e-01 3.42e-12 3.34e-02 2.69e-02
[1] "PP abf for shared variant: 2.69%"
Overlapping variants: 1297
Variants after allele harmonization: 1297
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.77e-13 9.38e-01 9.88e-15 3.34e-02 2.89e-02
[1] "PP abf for shared variant: 2.89%"
Overlapping variants: 1232
Variants after allele harmonization: 1232
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 1177
Variants after allele harmonization: 1177
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.958000 0.008120 0.033200 0.000280 0.000465
[1] "PP abf for shared variant: 0.0465%"
Overlapping variants: 1208
Variants after allele harmonization: 1208
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.15000 0.79200 0.00697 0.03680 0.01380
[1] "PP abf for shared variant: 1.38%"
Overlapping variants: 1560
Variants after allele harmonization: 1560
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.88100 0.06110 0.05110 0.00354 0.00312
[1] "PP abf for shared variant: 0.312%"
Overlapping variants: 1616
Variants after allele harmonization: 1616
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.84400 0.09620 0.05040 0.00575 0.00406
[1] "PP abf for shared variant: 0.406%"
Overlapping variants: 1644
Variants after allele harmonization: 1644
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.84200 0.09650 0.05130 0.00588 0.00467
[1] "PP abf for shared variant: 0.467%"
Overlapping variants: 1730
Variants after allele harmonization: 1730
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
6.07e-06 9.02e-01 3.88e-07 5.75e-02 4.02e-02
[1] "PP abf for shared variant: 4.02%"
Overlapping variants: 3361
Variants after allele harmonization: 3361
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004560 0.825000 0.000842 0.152000 0.017100
[1] "PP abf for shared variant: 1.71%"
Overlapping variants: 3388
Variants after allele harmonization: 3388
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.01e-09 7.65e-01 1.85e-10 1.41e-01 9.41e-02
[1] "PP abf for shared variant: 9.41%"
Overlapping variants: 2062
Variants after allele harmonization: 2062
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.23e-08 9.34e-01 1.66e-09 4.81e-02 1.83e-02
[1] "PP abf for shared variant: 1.83%"
Overlapping variants: 1666
Variants after allele harmonization: 1666
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.926000 0.019000 0.053400 0.001100 0.000639
[1] "PP abf for shared variant: 0.0639%"
Overlapping variants: 2687
Variants after allele harmonization: 2687
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.02e-24 4.84e-01 5.19e-24 5.00e-01 1.55e-02
[1] "PP abf for shared variant: 1.55%"
Overlapping variants: 1890
Variants after allele harmonization: 1890
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.73500 0.19400 0.05230 0.01380 0.00477
[1] "PP abf for shared variant: 0.477%"
Overlapping variants: 2374
Variants after allele harmonization: 2374
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.000232 0.898000 0.000019 0.073800 0.027500
[1] "PP abf for shared variant: 2.75%"
Overlapping variants: 3044
Variants after allele harmonization: 3044
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 2578
Variants after allele harmonization: 2578
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.33e-10 8.89e-01 6.95e-11 8.42e-02 2.72e-02
[1] "PP abf for shared variant: 2.72%"
Overlapping variants: 2175
Variants after allele harmonization: 2175
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.69e-16 8.95e-01 5.99e-17 6.97e-02 3.54e-02
[1] "PP abf for shared variant: 3.54%"
Overlapping variants: 1888
Variants after allele harmonization: 1888
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6650 0.2310 0.0669 0.0232 0.0131
[1] "PP abf for shared variant: 1.31%"
Overlapping variants: 2168
Variants after allele harmonization: 2168
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.010200 0.933000 0.000424 0.038800 0.017100
[1] "PP abf for shared variant: 1.71%"
Overlapping variants: 1904
Variants after allele harmonization: 1904
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.45e-04 8.92e-01 5.67e-05 9.28e-02 1.48e-02
[1] "PP abf for shared variant: 1.48%"
Overlapping variants: 1903
Variants after allele harmonization: 1903
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.72e-197 9.01e-01 2.65e-198 6.42e-02 3.48e-02
[1] "PP abf for shared variant: 3.48%"
Overlapping variants: 2031
Variants after allele harmonization: 2031
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.57600 0.35500 0.03770 0.02320 0.00736
[1] "PP abf for shared variant: 0.736%"
Overlapping variants: 1994
Variants after allele harmonization: 1994
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.06760 0.57700 0.03680 0.31400 0.00412
[1] "PP abf for shared variant: 0.412%"
Overlapping variants: 1229
Variants after allele harmonization: 1229
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1500 0.4860 0.0732 0.2380 0.0530
[1] "PP abf for shared variant: 5.3%"
Overlapping variants: 2959
Variants after allele harmonization: 2959
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
9.28e-09 9.13e-01 6.98e-10 6.87e-02 1.81e-02
[1] "PP abf for shared variant: 1.81%"
Overlapping variants: 3432
Variants after allele harmonization: 3432
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004460 0.880000 0.000481 0.095000 0.019900
[1] "PP abf for shared variant: 1.99%"
Overlapping variants: 1879
Variants after allele harmonization: 1879
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7500 0.1370 0.0868 0.0158 0.0101
[1] "PP abf for shared variant: 1.01%"
Overlapping variants: 2180
Variants after allele harmonization: 2180
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
6.77e-06 9.13e-01 3.66e-07 4.93e-02 3.74e-02
[1] "PP abf for shared variant: 3.74%"
Overlapping variants: 2183
Variants after allele harmonization: 2183
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.898000 0.007890 0.093300 0.000820 0.000322
[1] "PP abf for shared variant: 0.0322%"
Overlapping variants: 2827
Variants after allele harmonization: 2827
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.22e-08 8.98e-01 3.85e-09 6.62e-02 3.59e-02
[1] "PP abf for shared variant: 3.59%"
Overlapping variants: 2366
Variants after allele harmonization: 2366
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.67e-04 9.19e-01 4.35e-05 5.20e-02 2.83e-02
[1] "PP abf for shared variant: 2.83%"
Overlapping variants: 1327
Variants after allele harmonization: 1327
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.45e-08 6.38e-01 7.79e-09 3.44e-01 1.81e-02
[1] "PP abf for shared variant: 1.81%"
Overlapping variants: 2029
Variants after allele harmonization: 2029
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.39e-03 9.19e-01 9.04e-05 5.99e-02 1.92e-02
[1] "PP abf for shared variant: 1.92%"
Overlapping variants: 1447
Variants after allele harmonization: 1447
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.91900 0.02860 0.04980 0.00155 0.00155
[1] "PP abf for shared variant: 0.155%"
Overlapping variants: 2695
Variants after allele harmonization: 2695
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.17e-08 8.71e-01 7.90e-09 9.59e-02 3.31e-02
[1] "PP abf for shared variant: 3.31%"
Overlapping variants: 1323
Variants after allele harmonization: 1323
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0325 0.6130 0.0172 0.3250 0.0124
[1] "PP abf for shared variant: 1.24%"
Overlapping variants: 2534
Variants after allele harmonization: 2534
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.01e-07 8.28e-01 3.52e-08 1.45e-01 2.71e-02
[1] "PP abf for shared variant: 2.71%"
Overlapping variants: 2243
Variants after allele harmonization: 2243
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.87400 0.07010 0.05010 0.00401 0.00197
[1] "PP abf for shared variant: 0.197%"
Overlapping variants: 2809
Variants after allele harmonization: 2809
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.80e-09 8.39e-01 6.49e-10 6.97e-02 9.10e-02
[1] "PP abf for shared variant: 9.1%"
Overlapping variants: 2701
Variants after allele harmonization: 2701
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.61e-10 8.89e-01 4.74e-11 9.14e-02 2.00e-02
[1] "PP abf for shared variant: 2%"
Overlapping variants: 2708
Variants after allele harmonization: 2708
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.34e-13 8.82e-01 3.66e-14 9.66e-02 2.17e-02
[1] "PP abf for shared variant: 2.17%"
Overlapping variants: 1268
Variants after allele harmonization: 1268
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.25e-04 9.11e-01 1.92e-05 7.74e-02 1.14e-02
[1] "PP abf for shared variant: 1.14%"
Overlapping variants: 2526
Variants after allele harmonization: 2526
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.84700 0.09570 0.04950 0.00559 0.00246
[1] "PP abf for shared variant: 0.246%"
Overlapping variants: 2374
Variants after allele harmonization: 2374
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.74200 0.14400 0.09150 0.01780 0.00427
[1] "PP abf for shared variant: 0.427%"
Overlapping variants: 2152
Variants after allele harmonization: 2152
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.81900 0.09810 0.07080 0.00848 0.00386
[1] "PP abf for shared variant: 0.386%"
Overlapping variants: 2536
Variants after allele harmonization: 2536
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
9.38e-09 7.35e-01 1.74e-09 1.36e-01 1.29e-01
[1] "PP abf for shared variant: 12.9%"
Overlapping variants: 2669
Variants after allele harmonization: 2669
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.7340 0.0000 0.2510 0.0148
[1] "PP abf for shared variant: 1.48%"
Overlapping variants: 1881
Variants after allele harmonization: 1881
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.003230 0.901000 0.000217 0.060500 0.034900
[1] "PP abf for shared variant: 3.49%"
Overlapping variants: 2158
Variants after allele harmonization: 2158
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.41700 0.52200 0.02290 0.02870 0.00887
[1] "PP abf for shared variant: 0.887%"
Overlapping variants: 1518
Variants after allele harmonization: 1518
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72500 0.20500 0.04780 0.01350 0.00802
[1] "PP abf for shared variant: 0.802%"
Overlapping variants: 2704
Variants after allele harmonization: 2704
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.06e-09 9.17e-01 1.85e-10 5.53e-02 2.81e-02
[1] "PP abf for shared variant: 2.81%"
Overlapping variants: 2275
Variants after allele harmonization: 2275
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.67300 0.14500 0.14400 0.03100 0.00664
[1] "PP abf for shared variant: 0.664%"
Overlapping variants: 2089
Variants after allele harmonization: 2089
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.64500 0.28400 0.04490 0.01980 0.00612
[1] "PP abf for shared variant: 0.612%"
Overlapping variants: 1346
Variants after allele harmonization: 1346
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5970 0.0389 0.3290 0.0214 0.0134
[1] "PP abf for shared variant: 1.34%"
Overlapping variants: 2562
Variants after allele harmonization: 2562
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.72500 0.18400 0.06730 0.01710 0.00674
[1] "PP abf for shared variant: 0.674%"
Overlapping variants: 1955
Variants after allele harmonization: 1955
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
6.57e-06 9.12e-01 4.90e-07 6.81e-02 1.98e-02
[1] "PP abf for shared variant: 1.98%"
Overlapping variants: 3839
Variants after allele harmonization: 3839
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.38e-08 8.70e-01 2.89e-09 1.06e-01 2.43e-02
[1] "PP abf for shared variant: 2.43%"
Overlapping variants: 2489
Variants after allele harmonization: 2489
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.83800 0.10200 0.05060 0.00617 0.00321
[1] "PP abf for shared variant: 0.321%"
Overlapping variants: 1910
Variants after allele harmonization: 1910
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.05100 0.85800 0.00395 0.06640 0.02120
[1] "PP abf for shared variant: 2.12%"
Overlapping variants: 3671
Variants after allele harmonization: 3671
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.31e-55 8.16e-01 4.40e-56 1.55e-01 2.90e-02
[1] "PP abf for shared variant: 2.9%"
Overlapping variants: 2306
Variants after allele harmonization: 2306
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7170 0.1050 0.1440 0.0212 0.0126
[1] "PP abf for shared variant: 1.26%"
Overlapping variants: 2977
Variants after allele harmonization: 2977
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.55100 0.38000 0.03590 0.02480 0.00784
[1] "PP abf for shared variant: 0.784%"
Overlapping variants: 2686
Variants after allele harmonization: 2686
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.4040 0.1030 0.3750 0.0961 0.0216
[1] "PP abf for shared variant: 2.16%"
Overlapping variants: 2829
Variants after allele harmonization: 2829
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.50e-04 8.96e-01 7.11e-05 8.49e-02 1.86e-02
[1] "PP abf for shared variant: 1.86%"
Overlapping variants: 2572
Variants after allele harmonization: 2572
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8270 0.0000 0.1470 0.0259
[1] "PP abf for shared variant: 2.59%"
Overlapping variants: 2053
Variants after allele harmonization: 2053
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.37e-43 9.09e-01 1.72e-44 6.61e-02 2.53e-02
[1] "PP abf for shared variant: 2.53%"
Overlapping variants: 2425
Variants after allele harmonization: 2425
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.40e-54 8.16e-01 4.61e-55 1.57e-01 2.71e-02
[1] "PP abf for shared variant: 2.71%"
Overlapping variants: 2029
Variants after allele harmonization: 2029
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.6330 0.2820 0.0412 0.0183 0.0253
[1] "PP abf for shared variant: 2.53%"
Overlapping variants: 2046
Variants after allele harmonization: 2046
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7670 0.1600 0.0557 0.0116 0.0053
[1] "PP abf for shared variant: 0.53%"
Overlapping variants: 4131
Variants after allele harmonization: 4131
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.59e-09 8.75e-01 4.16e-10 1.01e-01 2.35e-02
[1] "PP abf for shared variant: 2.35%"
Overlapping variants: 2242
Variants after allele harmonization: 2242
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.003670 0.880000 0.000258 0.061700 0.054200
[1] "PP abf for shared variant: 5.42%"
Overlapping variants: 2518
Variants after allele harmonization: 2518
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.14100 0.70000 0.00805 0.03980 0.11100
[1] "PP abf for shared variant: 11.1%"
Overlapping variants: 2736
Variants after allele harmonization: 2736
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7150 0.2090 0.0541 0.0158 0.0055
[1] "PP abf for shared variant: 0.55%"
Overlapping variants: 2130
Variants after allele harmonization: 2130
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.85800 0.07280 0.06180 0.00524 0.00270
[1] "PP abf for shared variant: 0.27%"
Overlapping variants: 1674
Variants after allele harmonization: 1674
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.936000 0.005110 0.058100 0.000317 0.000179
[1] "PP abf for shared variant: 0.0179%"
Overlapping variants: 3259
Variants after allele harmonization: 3259
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.002510 0.798000 0.000483 0.153000 0.045300
[1] "PP abf for shared variant: 4.53%"
Overlapping variants: 2949
Variants after allele harmonization: 2949
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.66500 0.23500 0.06710 0.02370 0.00894
[1] "PP abf for shared variant: 0.894%"
Overlapping variants: 1925
Variants after allele harmonization: 1925
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.521000 0.002100 0.475000 0.001910 0.000889
[1] "PP abf for shared variant: 0.0889%"
Overlapping variants: 2808
Variants after allele harmonization: 2808
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.37e-22 9.08e-01 9.96e-24 6.59e-02 2.64e-02
[1] "PP abf for shared variant: 2.64%"
Overlapping variants: 2634
Variants after allele harmonization: 2634
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.003440 0.752000 0.000988 0.216000 0.027000
[1] "PP abf for shared variant: 2.7%"
Overlapping variants: 2846
Variants after allele harmonization: 2846
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.62900 0.27600 0.05990 0.02630 0.00882
[1] "PP abf for shared variant: 0.882%"
Overlapping variants: 2552
Variants after allele harmonization: 2552
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.75900 0.18300 0.04410 0.01060 0.00347
[1] "PP abf for shared variant: 0.347%"
Overlapping variants: 1789
Variants after allele harmonization: 1789
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.90500 0.03240 0.05930 0.00213 0.00107
[1] "PP abf for shared variant: 0.107%"
Overlapping variants: 2390
Variants after allele harmonization: 2390
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.005110 0.906000 0.000421 0.074600 0.014100
[1] "PP abf for shared variant: 1.41%"
Overlapping variants: 2013
Variants after allele harmonization: 2013
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.29100 0.63900 0.01890 0.04160 0.00944
[1] "PP abf for shared variant: 0.944%"
Overlapping variants: 2676
Variants after allele harmonization: 2676
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8990 0.0000 0.0734 0.0275
[1] "PP abf for shared variant: 2.75%"
Overlapping variants: 1480
Variants after allele harmonization: 1480
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.82100 0.12300 0.04490 0.00672 0.00444
[1] "PP abf for shared variant: 0.444%"
Overlapping variants: 1819
Variants after allele harmonization: 1819
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004530 0.876000 0.000517 0.099900 0.019500
[1] "PP abf for shared variant: 1.95%"
Overlapping variants: 2088
Variants after allele harmonization: 2088
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.018500 0.917000 0.000972 0.048300 0.014900
[1] "PP abf for shared variant: 1.49%"
Overlapping variants: 1370
Variants after allele harmonization: 1370
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.60600 0.00367 0.38700 0.00234 0.00123
[1] "PP abf for shared variant: 0.123%"
Overlapping variants: 2012
Variants after allele harmonization: 2012
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.02560 0.85900 0.00166 0.05580 0.05780
[1] "PP abf for shared variant: 5.78%"
Overlapping variants: 2025
Variants after allele harmonization: 2025
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.22e-198 9.21e-01 2.75e-199 5.99e-02 1.86e-02
[1] "PP abf for shared variant: 1.86%"
Overlapping variants: 3202
Variants after allele harmonization: 3202
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8190 0.0000 0.1630 0.0183
[1] "PP abf for shared variant: 1.83%"
Overlapping variants: 2542
Variants after allele harmonization: 2542
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
8.42e-01 4.68e-05 1.58e-01 8.75e-06 2.89e-06
[1] "PP abf for shared variant: 0.000289%"
Overlapping variants: 2704
Variants after allele harmonization: 2704
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7640 0.1280 0.0841 0.0141 0.0097
[1] "PP abf for shared variant: 0.97%"
Overlapping variants: 2174
Variants after allele harmonization: 2174
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01730 0.87200 0.00169 0.08520 0.02380
[1] "PP abf for shared variant: 2.38%"
Overlapping variants: 3204
Variants after allele harmonization: 3204
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7620 0.0599 0.1530 0.0120 0.0130
[1] "PP abf for shared variant: 1.3%"
Overlapping variants: 3145
Variants after allele harmonization: 3145
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
6.70e-31 8.23e-01 1.26e-31 1.55e-01 2.21e-02
[1] "PP abf for shared variant: 2.21%"
Overlapping variants: 1959
Variants after allele harmonization: 1959
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 3203
Variants after allele harmonization: 3203
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.002660 0.813000 0.000531 0.162000 0.021800
[1] "PP abf for shared variant: 2.18%"
Overlapping variants: 2391
Variants after allele harmonization: 2391
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.74100 0.17500 0.06110 0.01450 0.00802
[1] "PP abf for shared variant: 0.802%"
Overlapping variants: 3044
Variants after allele harmonization: 3044
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.67e-06 8.65e-01 2.83e-07 9.17e-02 4.28e-02
[1] "PP abf for shared variant: 4.28%"
Overlapping variants: 1416
Variants after allele harmonization: 1416
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.3320 0.2370 0.2380 0.1700 0.0227
[1] "PP abf for shared variant: 2.27%"
Overlapping variants: 2536
Variants after allele harmonization: 2536
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.1190 0.6900 0.0222 0.1290 0.0401
[1] "PP abf for shared variant: 4.01%"
Overlapping variants: 3294
Variants after allele harmonization: 3294
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8830 0.0000 0.0926 0.0239
[1] "PP abf for shared variant: 2.39%"
Overlapping variants: 2040
Variants after allele harmonization: 2040
Alleles flipped: 0
[2025-12-30 00:51:01,840] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:51:01,840] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:51:01,841] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Es gab 50 oder mehr Warnungen (Anzeige der ersten 50 mit warnings())
[2025-12-30 00:51:01,841] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]:
Error processing ENSG00000273387: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 2301
Variants after allele harmonization: 2301
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.002160 0.804000 0.000434 0.162000 0.031800
[1] "PP abf for shared variant: 3.18%"
Overlapping variants: 2021
Variants after allele harmonization: 2021
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.83500 0.11000 0.04550 0.00600 0.00384
[1] "PP abf for shared variant: 0.384%"
Overlapping variants: 1022
Variants after allele harmonization: 1022
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.19e-10 9.25e-01 6.41e-12 4.99e-02 2.46e-02
[1] "PP abf for shared variant: 2.46%"
Overlapping variants: 683
Variants after allele harmonization: 683
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.922000 0.030800 0.045200 0.001510 0.000759
[1] "PP abf for shared variant: 0.0759%"
Overlapping variants: 1894
Variants after allele harmonization: 1894
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.51500 0.44100 0.02020 0.01730 0.00665
[1] "PP abf for shared variant: 0.665%"
Overlapping variants: 1775
Variants after allele harmonization: 1775
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.953000 0.007240 0.039500 0.000300 0.000201
[1] "PP abf for shared variant: 0.0201%"
Overlapping variants: 2894
Variants after allele harmonization: 2894
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.5590 0.3270 0.0615 0.0359 0.0166
[1] "PP abf for shared variant: 1.66%"
Overlapping variants: 2503
Variants after allele harmonization: 2503
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
6.66e-05 8.70e-01 6.86e-06 8.96e-02 4.05e-02
[1] "PP abf for shared variant: 4.05%"
Overlapping variants: 1324
Variants after allele harmonization: 1324
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.86500 0.07240 0.04290 0.00358 0.01600
[1] "PP abf for shared variant: 1.6%"
Overlapping variants: 677
Variants after allele harmonization: 677
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.81000 0.13600 0.03960 0.00661 0.00794
[1] "PP abf for shared variant: 0.794%"
Overlapping variants: 3108
Variants after allele harmonization: 3108
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.7290 0.1020 0.1360 0.0190 0.0145
[1] "PP abf for shared variant: 1.45%"
Overlapping variants: 2068
Variants after allele harmonization: 2068
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.9020 0.0000 0.0514 0.0466
[1] "PP abf for shared variant: 4.66%"
Overlapping variants: 1638
Variants after allele harmonization: 1638
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.42e-50 9.22e-01 1.64e-51 4.43e-02 3.41e-02
[1] "PP abf for shared variant: 3.41%"
Overlapping variants: 1950
Variants after allele harmonization: 1950
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.43e-05 9.00e-01 3.45e-06 5.72e-02 4.25e-02
[1] "PP abf for shared variant: 4.25%"
Overlapping variants: 2049
Variants after allele harmonization: 2049
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
NaN NaN NaN NaN NaN
[1] "PP abf for shared variant: NaN%"
Overlapping variants: 3065
Variants after allele harmonization: 3065
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.24e-15 8.99e-01 4.77e-16 8.17e-02 1.96e-02
[1] "PP abf for shared variant: 1.96%"
Overlapping variants: 2220
Variants after allele harmonization: 2220
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
1.06e-12 9.20e-01 7.55e-14 6.56e-02 1.46e-02
[1] "PP abf for shared variant: 1.46%"
Overlapping variants: 1890
Variants after allele harmonization: 1890
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.004660 0.934000 0.000181 0.036300 0.024900
[1] "PP abf for shared variant: 2.49%"
Overlapping variants: 3211
Variants after allele harmonization: 3211
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.48e-10 8.19e-01 1.08e-10 1.62e-01 1.91e-02
[1] "PP abf for shared variant: 1.91%"
Overlapping variants: 2604
Variants after allele harmonization: 2604
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8900 0.0000 0.0788 0.0309
[1] "PP abf for shared variant: 3.09%"
Overlapping variants: 3213
Variants after allele harmonization: 3213
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.01e-09 8.19e-01 3.85e-10 1.57e-01 2.39e-02
[1] "PP abf for shared variant: 2.39%"
Overlapping variants: 2162
Variants after allele harmonization: 2162
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.01760 0.90000 0.00124 0.06360 0.01730
[1] "PP abf for shared variant: 1.73%"
Overlapping variants: 2195
Variants after allele harmonization: 2195
Alleles flipped: 0
[2025-12-30 00:51:04,694] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:51:04,695] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:51:04,695] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Es gab 30 Warnungen (Anzeige mit warnings())
[2025-12-30 00:51:04,696] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]:
Error processing ENSG00000279714: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 1779
Variants after allele harmonization: 1779
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.009570 0.929000 0.000408 0.039600 0.021300
[1] "PP abf for shared variant: 2.13%"
Overlapping variants: 2068
Variants after allele harmonization: 2068
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.91000 0.02570 0.06180 0.00174 0.00122
[1] "PP abf for shared variant: 0.122%"
Overlapping variants: 1775
Variants after allele harmonization: 1775
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.02910 0.88900 0.00199 0.06100 0.01930
[1] "PP abf for shared variant: 1.93%"
Overlapping variants: 3320
Variants after allele harmonization: 3320
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
7.59e-20 8.55e-01 7.42e-21 8.36e-02 6.13e-02
[1] "PP abf for shared variant: 6.13%"
Overlapping variants: 2638
Variants after allele harmonization: 2638
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.80200 0.13900 0.04800 0.00831 0.00320
[1] "PP abf for shared variant: 0.32%"
Overlapping variants: 2686
Variants after allele harmonization: 2686
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.06e-26 8.77e-01 3.25e-27 9.31e-02 3.01e-02
[1] "PP abf for shared variant: 3.01%"
Overlapping variants: 3109
Variants after allele harmonization: 3109
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
5.33e-24 8.59e-01 4.95e-25 7.97e-02 6.15e-02
[1] "PP abf for shared variant: 6.15%"
Overlapping variants: 1458
Variants after allele harmonization: 1458
Alleles flipped: 0
[2025-12-30 00:51:05,696] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:51:05,696] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:51:05,697] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Warnmeldungen:
[2025-12-30 00:51:05,697] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 1:
[2025-12-30 00:51:05,697] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,698] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.016814
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,698] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 2:
[2025-12-30 00:51:05,698] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset1, 1) :
[2025-12-30 00:51:05,699] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.0020226
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,699] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 3:
[2025-12-30 00:51:05,699] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,700] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.0020482
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,700] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 4:
[2025-12-30 00:51:05,700] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,700] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 7.2563e-05
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,701] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 5:
[2025-12-30 00:51:05,701] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,701] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.00058231
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,702] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 6:
[2025-12-30 00:51:05,702] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset1, 1) :
[2025-12-30 00:51:05,702] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 3.3539e-05
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,702] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 7:
[2025-12-30 00:51:05,703] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,703] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.0013637
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,703] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 8:
[2025-12-30 00:51:05,703] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,704] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.0013687
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
[2025-12-30 00:51:05,704] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: 9:
[2025-12-30 00:51:05,704] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,704] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 0.00058231
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
Error processing ENSG00000281530: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 2754
Variants after allele harmonization: 2754
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0144 0.4670 0.0149 0.4820 0.0218
[1] "PP abf for shared variant: 2.18%"
Overlapping variants: 2063
Variants after allele harmonization: 2063
Alleles flipped: 0
[2025-12-30 00:51:05,966] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
[2025-12-30 00:51:05,966] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Zusätzlich:
[2025-12-30 00:51:05,966] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: Warnmeldung:
[2025-12-30 00:51:05,967] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: In check_dataset(d = dataset2, 2) :
[2025-12-30 00:51:05,967] WARNING:rpy2.rinterface_lib.callbacks: R[write to console]: minimum p value is: 2.2803e-05
If this is what you expected, this is not a problem.
If this is not as small as you expected, please check the 02_data vignette.
Error processing ENSG00000282602: Fehler in check_dataset(d = dataset1, 1) :
dataset 1: varbeta contains missing values
Overlapping variants: 2436
Variants after allele harmonization: 2436
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.74300 0.17400 0.06180 0.01450 0.00592
[1] "PP abf for shared variant: 0.592%"
Overlapping variants: 1964
Variants after allele harmonization: 1964
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.02e-11 9.20e-01 1.53e-12 3.51e-02 4.46e-02
[1] "PP abf for shared variant: 4.46%"
Overlapping variants: 4399
Variants after allele harmonization: 4399
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.39e-09 8.58e-01 2.96e-10 1.06e-01 3.56e-02
[1] "PP abf for shared variant: 3.56%"
Overlapping variants: 2822
Variants after allele harmonization: 2822
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.0000 0.8820 0.0000 0.0835 0.0341
[1] "PP abf for shared variant: 3.41%"
Overlapping variants: 2177
Variants after allele harmonization: 2177
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
2.30e-17 9.03e-01 1.56e-18 6.12e-02 3.53e-02
[1] "PP abf for shared variant: 3.53%"
Overlapping variants: 2267
Variants after allele harmonization: 2267
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
4.10e-05 9.31e-01 2.16e-06 4.91e-02 1.94e-02
[1] "PP abf for shared variant: 1.94%"
Overlapping variants: 2191
Variants after allele harmonization: 2191
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
3.99e-201 8.86e-01 3.14e-202 6.97e-02 4.38e-02
[1] "PP abf for shared variant: 4.38%"
Overlapping variants: 2070
Variants after allele harmonization: 2070
Alleles flipped: 0
PP.H0.abf PP.H1.abf PP.H2.abf PP.H3.abf PP.H4.abf
0.08630 0.82300 0.00578 0.05510 0.02990
[1] "PP abf for shared variant: 2.99%"
Genome-wide Colocalization Summary:
Genes tested: 438
PP.H4 >= 0.5: 1
PP.H4 >= 0.8 (strong): 0
coloc_results
| gene_id | gene_name | chr | start | end | n_snps | PP.H0 | PP.H1 | PP.H2 | PP.H3 | PP.H4 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 259 | ENSG00000186998 | ENSG00000186998 | 22 | 29205896.0 | 29259597.0 | 2125 | 1.015944e-16 | 0.311081 | 5.492107e-17 | 0.167646 | 0.521273 |
| 2 | ENSG00000025770 | ENSG00000025770 | 22 | 50508224.0 | 50524780.0 | 2493 | 1.316848e-04 | 0.694187 | 1.119525e-05 | 0.058770 | 0.246901 |
| 164 | ENSG00000128159 | ENSG00000128159 | 22 | 50217689.0 | 50245023.0 | 3255 | 2.366452e-05 | 0.642525 | 4.756293e-06 | 0.128912 | 0.228535 |
| 115 | ENSG00000100298 | ENSG00000100298 | 22 | 39097224.0 | 39104067.0 | 2080 | 1.417083e-50 | 0.759303 | 9.827111e-52 | 0.052468 | 0.188229 |
| 229 | ENSG00000183773 | ENSG00000183773 | 22 | 20965108.0 | 20981360.0 | 1508 | 7.370555e-01 | 0.051550 | 4.849696e-02 | 0.003232 | 0.159665 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 197 | ENSG00000161180 | ENSG00000161180 | 22 | 21632716.0 | 21637329.0 | 1416 | NaN | NaN | NaN | NaN | NaN |
| 295 | ENSG00000211660 | ENSG00000211660 | 22 | 22697789.0 | 22698407.0 | 1232 | NaN | NaN | NaN | NaN | NaN |
| 309 | ENSG00000218357 | ENSG00000218357 | 22 | 47402297.0 | 47488149.0 | 3044 | NaN | NaN | NaN | NaN | NaN |
| 393 | ENSG00000273216 | ENSG00000273216 | 22 | 29316744.0 | 29317220.0 | 1959 | NaN | NaN | NaN | NaN | NaN |
| 414 | ENSG00000279110 | ENSG00000279110 | 22 | 25052122.0 | 25065241.0 | 2049 | NaN | NaN | NaN | NaN | NaN |
438 rows × 11 columns
Visualize Colocalization Results#
Let’s create visualizations to interpret the colocalization findings. We now investigate the results for PP.H4, which can be interpreted as the following:
PP.H4 > 0.8: Strong evidence for colocalization (eQTL and GWAS signals likely share a causal variant) - prioritize for follow-up
PP.H4 0.5-0.8: Moderate evidence - may warrant additional investigation
PP.H3 > 0.8: Strong evidence for independent signals - both eQTL and GWAS exist but driven by different variants
Low all PPs: Insufficient power or weak signals
As we can see, we only identify one gene in our dummy dataset with a moderate colocalization between eQTL and GWAS hits and no colocalization with strong evidence between eQTL and GWAS hits. Please note, that this is due to subsampling of the original dataset.
fig, axes = plt.subplots(1, 2, figsize=(12, 5))
axes[0].hist(coloc_results["PP.H4"], bins=20, edgecolor="black", alpha=0.7)
axes[0].axvline(0.8, color="red", linestyle="--", label="Strong evidence")
axes[0].axvline(0.5, color="orange", linestyle="--", label="Moderate evidence")
axes[0].set_xlabel("PP.H4 (Colocalization)")
axes[0].set_ylabel("Number of Genes")
axes[0].set_title("Distribution of Colocalization Evidence")
axes[0].legend()
pp_cols = ["PP.H0", "PP.H1", "PP.H2", "PP.H3", "PP.H4"]
pp_means = coloc_results[pp_cols].mean()
axes[1].bar(range(len(pp_means)), pp_means.values)
axes[1].set_xticks(range(len(pp_means)))
axes[1].set_xticklabels(["H0", "H1\n(eQTL)", "H2\n(GWAS)", "H3\n(Both)", "H4\n(Coloc)"])
axes[1].set_ylabel("Mean Posterior Probability")
axes[1].set_title("Average Evidence Across All Genes")
plt.tight_layout()
plt.show()
if len(coloc_results[coloc_results["PP.H4"] >= 0.8]) > 0:
print("\nGenes with Strong Colocalization Evidence (PP.H4 >= 0.8):")
strong_coloc = coloc_results[coloc_results["PP.H4"] >= 0.8][["gene_id", "gene_name", "n_snps", "PP.H4", "PP.H3"]]
print(strong_coloc.to_string(index=False))
Integration with cellink: Storing Results#
Now let’s add the colocalization results back to our DonorData object for easy integration with downstream analyses.
def add_coloc_results_to_cellink(dd, coloc_results, gwas_trait_name="CAD"):
"""
Add colocalization results to the DonorData C.var annotations.
"""
coloc_cols = {
"PP.H4": f"coloc_{gwas_trait_name}_PP_H4",
"PP.H3": f"coloc_{gwas_trait_name}_PP_H3",
"PP.H2": f"coloc_{gwas_trait_name}_PP_H2",
"PP.H1": f"coloc_{gwas_trait_name}_PP_H1",
"PP.H0": f"coloc_{gwas_trait_name}_PP_H0",
"n_snps": f"coloc_{gwas_trait_name}_n_snps",
}
for new_col in coloc_cols.values():
dd.C.var[new_col] = np.nan
for _, row in coloc_results.iterrows():
gene_id = row["gene_id"]
if gene_id in dd.C.var.index:
for old_col, new_col in coloc_cols.items():
dd.C.var.loc[gene_id, new_col] = row[old_col]
classification_col = f"coloc_{gwas_trait_name}_class"
dd.C.var[classification_col] = "not_tested"
pp_h4_col = coloc_cols["PP.H4"]
tested_genes = dd.C.var[pp_h4_col].notna()
dd.C.var.loc[tested_genes & (dd.C.var[pp_h4_col] >= 0.8), classification_col] = "strong_coloc"
dd.C.var.loc[tested_genes & (dd.C.var[pp_h4_col] >= 0.5) & (dd.C.var[pp_h4_col] < 0.8), classification_col] = (
"moderate_coloc"
)
dd.C.var.loc[tested_genes & (dd.C.var[pp_h4_col] < 0.5), classification_col] = "no_coloc"
print("\nAdded colocalization results to dd.C.var:")
print(f" Columns added: {list(coloc_cols.values())}")
print(f" Classification column: {classification_col}")
print("\nColocalization Summary:")
print(dd.C.var[classification_col].value_counts())
return dd
dd = add_coloc_results_to_cellink(dd, coloc_results, gwas_trait_name="CAD")
print("\nGene annotations with colocalization results:")
coloc_annot_cols = [col for col in dd.C.var.columns if "coloc_" in col]
print(dd.C.var[coloc_annot_cols].loc[coloc_results["gene_id"]].head(10))
Added colocalization results to dd.C.var:
Columns added: ['coloc_CAD_PP_H4', 'coloc_CAD_PP_H3', 'coloc_CAD_PP_H2', 'coloc_CAD_PP_H1', 'coloc_CAD_PP_H0', 'coloc_CAD_n_snps']
Classification column: coloc_CAD_class
Colocalization Summary:
coloc_CAD_class
not_tested 441
no_coloc 429
moderate_coloc 1
Name: count, dtype: int64
Gene annotations with colocalization results:
coloc_CAD_PP_H4 coloc_CAD_PP_H3 coloc_CAD_PP_H2 \
Geneid
ENSG00000186998 0.521273 0.167646 5.492107e-17
ENSG00000025770 0.246901 0.058770 1.119525e-05
ENSG00000128159 0.228535 0.128912 4.756293e-06
ENSG00000100298 0.188229 0.052468 9.827111e-52
ENSG00000183773 0.159665 0.003232 4.849696e-02
ENSG00000236499 0.128672 0.136431 1.742348e-09
ENSG00000249222 0.111019 0.039781 8.047782e-03
ENSG00000177663 0.098264 0.052179 1.416414e-07
ENSG00000177993 0.094909 0.148687 7.674841e-05
ENSG00000213279 0.094131 0.140786 1.854002e-10
coloc_CAD_PP_H1 coloc_CAD_PP_H0 coloc_CAD_n_snps \
Geneid
ENSG00000186998 0.311081 1.015944e-16 2125.0
ENSG00000025770 0.694187 1.316848e-04 2493.0
ENSG00000128159 0.642525 2.366452e-05 3255.0
ENSG00000100298 0.759303 1.417083e-50 2080.0
ENSG00000183773 0.051550 7.370555e-01 1508.0
ENSG00000236499 0.734897 9.376481e-09 2536.0
ENSG00000249222 0.699946 1.412063e-01 2518.0
ENSG00000177663 0.849555 2.301813e-06 2338.0
ENSG00000177993 0.755938 3.899463e-04 1958.0
ENSG00000213279 0.765083 1.006860e-09 3388.0
coloc_CAD_class
Geneid
ENSG00000186998 moderate_coloc
ENSG00000025770 no_coloc
ENSG00000128159 no_coloc
ENSG00000100298 no_coloc
ENSG00000183773 no_coloc
ENSG00000236499 no_coloc
ENSG00000249222 no_coloc
ENSG00000177663 no_coloc
ENSG00000177993 no_coloc
ENSG00000213279 no_coloc