pylimma.kegga

pylimma.kegga(de, gene_pathway, pathway_names=None, universe=None, *, species=None, prior_prob=None, covariate=None, plot=False, fdr=0.05, trend=False, **kwargs)[source]

KEGG pathway over-representation analysis.

Port of R limma’s kegga (kegga.R). See module docstring for the gene_pathway format and the Phase-1 scope cuts.

All parameters except pathway_names have identical semantics to goana(); see that function’s docstring for full descriptions.

Parameters:: pathway_names (DataFrame, optional) – Two-column mapping from pathway id (column 0) to human-readable description (column 1). If absent, the output’s pathway column repeats the pathway id verbatim.
Return type:: DataFrame