idea.run_gsea

idea.run_gsea(genes: list | ndarray, library: str = 'BP', threshold: float | None = 0.05, background: list | ndarray | None = None, use_pvalue: bool = False) → DataFrame

Run gene ontology analysis.

Parameters:

• genes (Union[list, np.ndarray]) – A list of genes to run gene ontology analysis on.

• library (str, optional) –

  The gene ontology library to use. One of Enrichr.LIBRARIES. Shortcuts for:

  • BP: GO_Biological_Process_2023

  • CC: GO_Cellular_Component_2023

  • MF: GO_Molecular_Function_2023

  • msigdb: MSigDB_Hallmark_2020

  • kegg: KEGG_2021_Human

• threshold (Optional[float], optional) – The threshold to use for filtering the gene ontology terms by p-value. If None, no filtering is done.

• background (Optional[Union[list, np.ndarray]], optional) – The background genes to use for the gene ontology analysis.

• use_pvalue (bool, optional) – Whether to use the p-value or the adjusted p-value for filtering the gene ontology terms. (Default: using the adjusted p-value)

Return type:

pd.DataFrame