--- a
+++ b/man/getGeneMapping.Rd
@@ -0,0 +1,49 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/feature_processing.R
+\name{getGeneMapping}
+\alias{getGeneMapping}
+\title{Mapping between pathway encoded genes/proteins and different ID formats.}
+\usage{
+getGeneMapping(features, keytype, org = "hsapiens", returntype = "SYMBOL")
+}
+\arguments{
+\item{features}{List of identifiers to be mapped.}
+
+\item{keytype}{String specifying the ID type, e.g., "ENTREZID" or "UNIPROT".}
+
+\item{org}{String that defines the organism. Default: hsapiens
+Options: see \code{\link[multiGSEA]{getOrganisms}}}
+
+\item{returntype}{String that specifies the returning ID type. Default:
+SYMBOL, Options: SYMBOL, ENTREZID, UNIPROT, ENSEMBL, REFSEQ}
+}
+\value{
+List containing mapped gene/protein IDs.
+}
+\description{
+Function to retrieve the gene/protein identifier mapping. Ongoing from
+genes/proteins retrieved from pathway definitions, which often include two or
+more ID formats or a format that is not present in your omics measurement,
+this function maps those IDs to a given format. Depending on the organism,
+additional packages have to be installed.
+}
+\examples{
+features <- graphite::nodes(graphite::pathways("hsapiens", "kegg")[[1]])
+features <- gsub("ENTREZID:", "", features)
+keytype <- "ENTREZID"
+getGeneMapping(features, keytype)
+
+getGeneMapping(features, keytype, returntype = "UNIPROT")
+\donttest{
+features <- graphite::nodes(graphite::pathways("rnorvegicus", "reactome")[[1]])
+features <- gsub("UNIPROT:", "", features)
+getGeneMapping(features, keytype = "UNIPROT", org = "rnorvegicus")
+
+getGeneMapping(features,
+  keytype = "UNIPROT",
+  org = "rnorvegicus",
+  returntype = "ENSEMBL"
+)
+}
+
+}