cellink.tl.external.load_gsmap_results#
- cellink.tl.external.load_gsmap_results(workdir, sample_name, trait_name, annotation=None)#
Load gsMap output files into DataFrames.
Reads the spot-level spatial LDSC results and the region-level Cauchy combination results written by
gsmap quick_modeor the individual pipeline steps.- Parameters:
workdir (str or Path) – Working directory used when running gsMap (
--workdir).sample_name (str) – Sample name used when running gsMap (
--sample_name).trait_name (str) – Trait name used when running gsMap (
--trait_name).annotation (str, optional) – Annotation column name. Required to locate Cauchy combination results.
- Return type:
- Returns:
dict with keys: -
"spatial_ldsc": pd.DataFrame or NonePer-spot LDSC results with columns spot, beta, se, z, p.
"cauchy_combination"pd.DataFrame or NoneRegion-level aggregated p-values (p_cauchy, p_median).
"workdir": Path"report_path": Path or None
Examples
>>> results = load_gsmap_results( ... workdir="./gsmap_output", ... sample_name="V1_Adult_Mouse_Brain_Coronal", ... trait_name="IQ", ... annotation="domain", ... ) >>> spot_df = results["spatial_ldsc"] >>> cauchy_df = results["cauchy_combination"]