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sspa_ora

source 

sspa_ora(
   mat, metadata, pathways, DA_cutoff, DA_testtype = 'ttest',
   custom_background = None
)

Class for overrepresentation analysis

Attributes

  • mat (pd.DataFrame) : dataframe containing input metabolomics data
  • metadata (pd.Series) : series containing phenotype metadata e.g 'COVID', 'NON-COVID'
  • pathways (pd.DataFrame) : pathway dataframe containing compound identifiers
  • DA_cutoff (float) : pFDR cutoff for selecting differential metabolites e.g. 0.05 or 0.01
  • DA_testtype (str) : Test type for selecing differential metabolites. Can either be 'ttest' (default) for the independent students T-test or 'mwu' for the Mann Whitney U test, both as implemented in SciPy.
  • custom_background (list) : background list of identifiers, default is to use annotated compounds in input data (i.e. mat.columns)

Methods:

.over_representation_analysis

source 

.over_representation_analysis()

Function for over representation analysis using Fisher exact test (right tailed)

Returns

DataFrame of ORA results for each pathway, p-value, FDR p-value, hits ratio, coverage of pathway, and identifiers of differential metabolites