mira.tl.fetch_ontologies

mira.tl.fetch_ontologies(list_id, ontologies=['WikiPathways_2019_Human', 'WikiPathways_2019_Mouse', 'KEGG_2019_Human', 'KEGG_2019_Mouse', 'GO_Molecular_Function_2018', 'GO_Cellular_Component_2018', 'GO_Biological_Process_2018', 'BioPlanet_2019'])

Fetch enrichment results from ontologies.

Parameters

list_idstr

genelist ID returned by post_genelist

onotologiesIterable[str], default = mira.tl.LEGACY_ONTOLOGIES

Retrieve results for these ontologies. For a full list of ontologies, see Enrichr.

Returns

resultsdict

Dictionary with schema:

{
    <ontology> : {
        [
            {'rank' : <rank>,
            'term' : <term>,
            'pvalue' : <pval>,
            'zscore': <zscore>,
            'combined_score': <combined_score>,
            'genes': [<gene1>, ..., <geneN>],
            'adj_pvalue': <adj_pval>},
            ...,
        ]
    }
}

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