% 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")

}