networkcommons.data.omics.deseq2

networkcommons.data.omics.deseq2(counts, metadata, test_group, ref_group, sample_col='sample_ID', feature_col='gene_symbol', covariates=None)

Runs DESeq2 analysis on the given counts and metadata.

Parameters:

  • counts (pd.DataFrame) – The counts data with gene symbols as index.

  • metadata (pd.DataFrame) – The metadata with sample IDs as index.

  • test_group (str) – The name of the test group.

  • ref_group (str) – The name of the reference group.

  • sample_col (str, optional) – The name of the sample ID column in the metadata. Defaults to ‘sample_ID’.

  • feature_col (str, optional) – The name of the feature column in the counts data. Defaults to ‘gene_symbol’.

  • covariates (list, optional) – List of covariates to include in the analysis. Defaults to None.

Returns:

The results of the DESeq2 analysis as a data frame.

Return type:

pd.DataFrame