data.getMSEA: Metabolite set enrichment analysis (MSEA) (using a...
In BRL-BCM/MolEndoMatch: Molecular Phenotype Patient Matchmaking

A function that returns the pathway enrichment score for all perturbed metabolites in a patient's full metabolomic profile.

1 2	data.getMSEA(met.profile, type = "zscore", gene.profile = NULL, paths.hsa)

`met.profile`	- A character vector of a patient's metabolomic profile, including KEGG IDs and the associated z-score or p-value describing the level of the metabolite compared to controls.
`type`	- Either "p-value" or "z-score".
`gene.profile`	- Default set to NULL, meaning the default enrichment analysis only considers metabolites. However, if you have gene data, too, set this parameter to a character vector of the gene names with found variants in the patient's record. Gene IDs must be converted to Entrez Identifiers.
`paths.hsa`	- Which pathways do you want to test. The default is all 289 KEGG pathways.

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paths.hsa = list.files("/Library/Frameworks/R.framework/Versions/3.5/Resources/library/pathview/extdata", pattern=".xml")
paths.hsa = as.character(unlist(sapply(paths.hsa, function(i) unlist(strsplit(i, split=".xml"))[1])))
pathway.data = data.getMSEA(met.profile, "z-score", NULL, paths.hsa)