metapone

metapone is an innovative R/Bioconductor package to address critical challenges in pathway enrichment analysis for untargeted metabolomics data. Existing pathway testing algorithms often overlook the unique characteristics of untargeted metabolomics data, leading to issues such as matching uncertainty between data features and metabolites, limitations in analyzing positive and negative mode liquid chromatography-mass spectrometry (LC/MS) data simultaneously, and the incompleteness of pathways in individual software packages.
This package introduces two novel statistical tests within a single framework: (i) a weighted gene set enrichment analysis-type test and (ii) a permutation-based weighted hypergeometric test, both considering matching uncertainty. Metapone can combine positive- and negative-ion mode results in a unified testing scheme. To ensure comprehensiveness, the built-in pathways were manually curated from three reliable sources: Kyoto Encyclopedia of Genes and Genomes, Mummichog, and The Small Molecule Pathway Database.