Over Representation Methods

This module contains the functions to run Over Representation Analysis (ORA).

pathway_forte.pathway_enrichment.over_representation.read_fold_change_df(path)

Read csv with gene names, fold changes and their p-values.

Return type

DataFrame

pathway_forte.pathway_enrichment.over_representation.filter_p_value(df, p_value=True, cutoff=0.05)

Return significantly differentially expressed genes in fold change df.

pathway_forte.pathway_enrichment.over_representation.perform_hypergeometric_test(genes_to_test, pathway_dict, gene_universe=41714, apply_threshold=False, threshold=0.05)

Perform hypergeometric tests.

Parameters

• genes_to_test (Set[str]) – gene set to test against pathway

• pathway_dict (Mapping[str, Set[str]]) – pathway name to gene set

• gene_universe (int) – number of HGNC symbols

• apply_threshold (bool) – return only significant pathways

• threshold (float) – significance threshold (by default 0.05)

Return type

DataFrame