cellink.tl.external.estimate_heritability

cellink.tl.external.estimate_heritability(sumstats_file, ref_ld_chr, w_ld_chr, out_prefix, overlap_annot=False, frqfile_chr=None, not_m_5_50=False, print_coefficients=False, print_delete_vals=False, samp_prev=None, pop_prev=None, intercept_h2=None, no_intercept=False, run=True, runner=None, **kwargs)

Estimate SNP heritability using LD Score regression

Convenience wrapper around run_ldsc_heritability with validation and structured output.

Parameters:

• sumstats_file (str) – Path to munged summary statistics file (.sumstats.gz)

• ref_ld_chr (str) – Prefix for reference LD scores (with @, e.g., “baseline.”)

• w_ld_chr (str) – Prefix for regression weights (with @, e.g., “weights.”)

• out_prefix (str) – Prefix for output files

• overlap_annot (bool, default False) – Use overlapping annotation model

• frqfile_chr (str, optional) – Prefix for allele frequency files (required with overlap_annot)

• not_m_5_50 (bool, default False) – Don’t restrict to common SNPs for estimating h2

• print_coefficients (bool, default False) – Print coefficient estimates

• print_delete_vals (bool, default False) – Print delete values

• samp_prev (float, optional) – Sample prevalence (for binary traits)

• pop_prev (float, optional) – Population prevalence (for binary traits)

• intercept_h2 (float, optional) – Constrain the LD Score regression intercept

• no_intercept (bool, default False) – Force intercept to 1

• 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: - ‘log_file’: Path to log file (if run=True) - ‘files_created’: List of created files (if run=True) - ‘command’: Command string (if run=False)

Examples

>>> result = estimate_heritability(
...     sumstats_file="height_munged.sumstats.gz",
...     ref_ld_chr="baseline_v1.2/baseline.",
...     w_ld_chr="weights_hm3_no_hla/weights.",
...     out_prefix="height_h2",
... )