cellink.tl.external.estimate_ld_scores_from_donor_data

cellink.tl.external.estimate_ld_scores_from_donor_data(dd, out_prefix='ldscores', 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, cleanup_files=True, plink_export_kwargs=None, run=True, runner=None, **kwargs)

Estimate LD scores from DonorData object

This convenience function exports genotype data from DonorData to PLINK format, then computes LD scores.

Parameters:

• dd (DonorData) – DonorData object containing genotype information

• out_prefix (str, default "ldscores") – Prefix for output files (also used for temporary PLINK files)

• cleanup_files (bool, default True) – Whether to remove temporary PLINK files after computing LD scores

• plink_export_kwargs (dict, optional) – Additional keyword arguments to pass to to_plink()

• estimate_ld_scores_from_bimfile) (... (other parameters as in)

Return type:

dict[str, Any]

Returns:

dict Results dictionary (same as estimate_ld_scores_from_bimfile)

Examples

>>> result = estimate_ld_scores_from_donor_data(
...     dd=my_donor_data, out_prefix="my_ldscores", annot_file="immune_genes.annot.gz", ld_wind_cm=1.0
... )