getMetaboliteMapping: Mapping between pathway encoded metabolites and different...

In yigbt/multiGSEA: Combining GSEA-based pathway enrichment with multi omics data integration

Mapping between pathway encoded metabolites and different metabolite ID formats.

Description

Function to retrieve the metabolite identifier mapping. Ongoing from metabolites retrieved from pathway definitions, which often include two or more ID formats, this function maps those IDs to a given format. The complete mapping table based on Comptox Dashboard, PubChem, HMDB, and ChEBI is provided in the AnnotationHub package metaboliteIDmapping.

Usage

getMetaboliteMapping(features, keytype, returntype = "HMDB")

Arguments

features	List of identifiers to be mapped.
keytype	String specifying the ID type, e.g., "ChEBI" or "KEGGCOMP".
returntype	String that specifies the returning ID type. Default: HMDB Options: HMDB, CAS, DTXCID, DTXSID, SID, CID, ChEBI, KEGG, Drugbank

Value

List containing mapped gene/protein IDs.

Examples

features <- graphite::nodes(graphite::pathways("hsapiens", "kegg")[[1]], which = "metabolites")
features <- gsub("KEGGCOMP:", "", features)
keytype <- "KEGG"

getMetaboliteMapping(features, keytype)

getMetaboliteMapping(features, keytype = "KEGG", returntype = "CID")

yigbt/multiGSEA documentation built on April 28, 2023, 10:02 p.m.