% 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"

)

}

}