goatools.goea.go_enrichment_ns module

Runs Fisher’s exact test, as well as multiple corrections for each of: BP MF CC

class goatools.goea.go_enrichment_ns.GOEnrichmentStudyNS(pop, ns2assoc, godag, propagate_counts=True, alpha=.05, methods=None, **kws)

Bases: object

Runs Fisher’s exact test, as well as multiple corrections for each of: BP MF CC

run_study(study_ids, **kws)

Run GOEAs for each namespace, BP MF CC

wr_xlsx(fout_xlsx, goea_results, **kws)

Write to spreadsheet format

wr_tsv(fout_tsv, goea_results, **kws)

Write to spreadsheet format

wr_txt(fout_txt, goea_results, **kws)

Write to spreadsheet format

get_assoc()

Get a list of all GO sets in all (BP, MF, CC) associations