stat.getORA_Metabolon: Metabolite set enrichment analysis (MSEA) (using a...

In BRL-BCM/CTDext: Extension package for the CTD R package.

Metabolite set enrichment analysis (MSEA) (using a hypergeometric test) using pathway knowledge curated by Metabolon

Description

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

Usage

stat.getORA_Metabolon(
  met.profile,
  threshold = 3,
  type = "zscore",
  gene.profile = NULL
)

Arguments

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.
threshold	- A cutoff to select metabolites with a zscore > threshold or < -1*threshold.
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.

Examples

pathway.data = stat.getORA_Metabolon(met.profile, threhold=3, "z-score", NULL)

BRL-BCM/CTDext documentation built on May 7, 2022, 5:31 a.m.