cellink.tl.external.estimate_ld_scores_from_bimfile

cellink.tl.external.estimate_ld_scores_from_bimfile(bfile_prefix, out_prefix, ld_wind_cm=1.0, ld_wind_kb=None, ld_wind_snp=None, annot_file=None, thin_annot=False, print_snps=None, maf_min=0.01, run=True, runner=None, **kwargs)

Estimate LD scores from PLINK bfile (works with any bfile, including 1000G)

Parameters:

• bfile_prefix (str) – Path to PLINK binary files (without .bed/.bim/.fam extension)

• out_prefix (str) – Prefix for output files

• ld_wind_cm (float, default 1.0) – LD window size in centiMorgans

• ld_wind_kb (int, optional) – LD window size in kilobases (alternative to ld_wind_cm)

• ld_wind_snp (int, optional) – LD window size in number of SNPs (alternative to ld_wind_cm)

• annot_file (str, optional) – Annotation file for computing category-specific LD scores

• thin_annot (bool, default False) – Thin the annot file by removing columns with <1% SNPs

• print_snps (str, optional) – File with SNP IDs to restrict LD score computation

• maf_min (float, default 0.01) – Minimum MAF threshold

• run (bool, default True) – Whether to execute the command or just return it

• runner (LDSCRunner, optional) – Runner instance to use

• **kwargs – Additional arguments passed to ldsc.py

Return type:

dict[str, Any]

Returns:

dict Results dictionary with: - ‘ld_scores_file’: Path to LD scores file (if run=True) - ‘files_created’: List of created files (if run=True) - ‘command’: Command string (if run=False)

Examples

>>> # Using 1000G reference panel
>>> result = estimate_ld_scores_from_bimfile(
...     bfile_prefix="1000G_EUR_Phase3_plink/1000G.EUR.QC.22",
...     out_prefix="my_ldscores_chr22",
...     annot_file="immune_genes.22.annot.gz",
...     print_snps="hm3_snps.txt",
... )