mmcci.an.pathway_subset

mmcci.an.pathway_subset(sample: CCIData, assay: str = 'raw', gsea_results: DataFrame | None = None, terms: list | None = None, strict: bool = False, assay_name: str | None = None) → CCIData[source]

Subsets a sample to only include interactions between genes in a set of pathways.

Parameters:

  • sample (CCIData) – The sample to subset.

  • assay (str) (optional) – The assay to use for the subset. Defaults to ‘raw’.

  • gsea_results (pd.DataFrame) – The GSEA results to use to subset the sample.

  • terms (list) – The terms to subset the sample with.

  • strict (bool) – Whether to only include interactions between genes in the same pathway.

Returns:

The sample with an added assay containing the subsetted interactions.

Return type:

CCIdata