metapone

metapone performs pathway enrichment and joint pathway testing for untargeted LC/MS metabolomics within R/Bioconductor by integrating positive and negative ion modes and accounting for feature–metabolite matching uncertainty.

Key Features:

• Joint Pathway Testing: Integrates positive and negative ion mode LC/MS results into a single pathway-testing framework.
• Handling Matching Uncertainty: Implements two statistical tests — a weighted gene set enrichment analysis-type test and a permutation-based weighted hypergeometric test — to account for uncertainty when matching data features to metabolites.
• Comprehensive Pathway Database: Uses a manually curated pathway collection compiled from Kyoto Encyclopedia of Genes and Genomes (KEGG), Mummichog, and The Small Molecule Pathway Database.

Scientific Applications:

• Pathway enrichment in untargeted metabolomics: Detects enriched metabolic pathways from untargeted metabolomics data to support biological interpretation.
• Dual-mode LC/MS analysis: Enables simultaneous analysis of positive and negative mode LC/MS datasets to improve pathway detection in studies generating dual-mode data.

Methodology:

Implements novel statistical tests that incorporate matching uncertainty; integrates positive and negative ion mode LC/MS data for joint analysis; and employs manually curated pathway sets from KEGG, Mummichog, and The Small Molecule Pathway Database.