omicverse.metabol.mummichog_basic

omicverse.metabol.mummichog_basic#

omicverse.metabol.mummichog_basic(mz, pvalue, *, polarity='positive', ppm=10.0, significance_cutoff=0.05, n_perm=1000, min_overlap=2, pathways=None, mass_db=None, seed=0)[source]#

Pure-Python mummichog — pathway enrichment from m/z peaks.

Parameters:

  • mz (ndarray) – m/z value per peak.

  • pvalue (ndarray) – Per-peak p-value from the upstream univariate test. Peaks with pvalue < significance_cutoff are the “hit” set; the rest form the background.

  • polarity (str (default: 'positive')) – "positive" or "negative".

  • ppm (float (default: 10.0)) – Mass-matching tolerance in ppm. Default 10.

  • significance_cutoff (float (default: 0.05)) – Threshold that splits mz into hits vs background.

  • n_perm (int (default: 1000)) – Random permutations for the empirical null p-value. 1000 is fine for tutorials; bump to ≥10000 for publication.

  • min_overlap (int (default: 2)) – Skip pathways with fewer than this many overlapping compounds.

Returns:

pathway, overlap, set_size, pvalue (empirical), padj (BH), observed_score.

Return type:

pd.DataFrame

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