goatools.godag.prtfncs module

python %prog study.file population.file gene-association.file

This program returns P-values for functional enrichment in a cluster of study genes using Fisher’s exact test, and corrected for multiple testing (including Bonferroni, Holm, Sidak, and false discovery rate)

class goatools.godag.prtfncs.GoeaPrintFunctions

Bases: object

Functions for displaying GOEA results

static print_date(min_ratio=None, pval=0.05)

Print GOATOOLS version and the date the GOEA was run.

print_results(results, min_ratio=None, indent=False, pval=0.05, prt=sys.stdout)

Print GOEA results with some additional statistics calculated.

print_results_adj(results, indent=False, prt=sys.stdout)

Print GOEA results.

static get_prtflds_default(results)

Get default fields names. Used in printing GOEA results.

Researchers can control which fields they want to print in the GOEA results or they can use the default fields.

static get_adj_records(results, min_ratio=None, pval=0.05)

Return GOEA results with some additional statistics calculated.