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_mode or 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:

dict

Returns:

dict with keys: - "spatial_ldsc" : pd.DataFrame or None

Per-spot LDSC results with columns spot, beta, se, z, p.

• "cauchy_combination"pd.DataFrame or None

  Region-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"]