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sspa_gsea

source 

.sspa_gsea(
   mat, metadata, pathway_df, ranking_metric = 'signal_to_noise', min_entity = 2
)

Run GSEA using gseapy package by zqfang (https://github.com/zqfang/GSEApy)

Args

  • mat (pd.DataFrame) : dataframe containing input metabolomics data
  • metadata (pd.Series) : series containing phenotype metadata e.g 'COVID', 'NON-COVID'
  • pathway_df (pd.DataFrame) : GMT-like pathway dataframe containing compound identifiers
  • ranking_metric (str) : Ranking metric for molecules in GSEA. Default is signal-to-noise ratio. Other options are 't_test' and see GSEApy package https://github.com/zqfang/GSEApy/blob/2b5419e14615b6fd19a575ff065256dc7099bbec/gseapy/gsea.py#L135 for more options.
  • min_entity (int, optional) : minimum number of molecules mapping to pathways for GSEA to be performed. Defaults to 2.