cellink.tl.external.run_sclinker_heritability

cellink.tl.external.run_sclinker_heritability(ld_prefixes, sumstats_files, ref_ld_chr, w_ld_chr, out_dir, *, annotation_prefixes=None, frqfile_chr=None, runner=None)

Run S-LDSC --h2 --overlap-annot for every (program, strategy, trait).

Important: sc-linker uses --h2 (standard partitioned heritability), not --h2-cts. The --ref-ld-chr is baseline,{program_ldscore} and --overlap-annot is always used.

--overlap-annot requires that .annot.gz files exist at the same prefix as the LD score files. Cellink writes them to a separate annotations/ directory, so this function symlinks them into the LD score directory automatically via annotation_prefixes.

Parameters:

• ld_prefixes (dict[str, dict[str, str]]) – Output of compute_ld_scores_for_sclinker: {program: {strategy: ld_score_prefix}}.

• sumstats_files (list[str]) – List of munged .sumstats.gz files (use absolute paths so the path survives Singularity bind-mount remapping).

• ref_ld_chr (str) – Baseline-LD prefix (e.g. from get_1000genomes_ld_scores()).

• w_ld_chr (str) – Regression weights prefix.

• out_dir (str | Path) – Directory to write .log output files.

• annotation_prefixes (dict[str, dict[str, str]] | None (default: None)) – Output of genescores_to_annotations: {program: {strategy: annot_prefix}}. Pass this so LDSC can find the .annot.gz files for --overlap-annot. If None, the function infers the location by replacing ldscores with annotations in ld_prefix.

• frqfile_chr (str | None (default: None)) – Allele frequency file prefix (required with --overlap-annot).

• runner (default: None) – LDSCRunner instance. If None, uses the global runner.

Return type:

dict[str, dict[str, dict[str, str]]]

Returns:

dict {program: {strategy: {trait: log_path}}}.