--- a
+++ b/man/getMetaboliteMapping.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature_processing.R
+\name{getMetaboliteMapping}
+\alias{getMetaboliteMapping}
+\title{Mapping between pathway encoded metabolites and different metabolite ID
+formats.}
+\usage{
+getMetaboliteMapping(features, keytype, returntype = "HMDB")
+}
+\arguments{
+\item{features}{List of identifiers to be mapped.}
+
+\item{keytype}{String specifying the ID type, e.g., "ChEBI" or "KEGGCOMP".}
+
+\item{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.
+}
+\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 \href{https://comptox.epa.gov/dashboard}{Comptox
+Dashboard}, \href{https://pubchem.ncbi.nlm.nih.gov/}{PubChem},
+\href{https://hmdb.ca/}{HMDB}, and \href{https://www.ebi.ac.uk/chebi}{ChEBI}
+is provided in the AnnotationHub package metaboliteIDmapping.
+}
+\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")
+
+}