R: Convert gene identifiers

convertGeneIdentifiers {psichomics}

R Documentation

Convert gene identifiers

Description

Convert gene identifiers

Usage

convertGeneIdentifiers(annotation, genes, key = "ENSEMBL",
  target = "SYMBOL", ignoreDuplicatedTargets = TRUE)

Arguments

`annotation`	OrgDb: genome wide annotation for an organism, e.g. `org.Hs.eg.db`
`genes`	Character: genes to be converted
`key`	Character: type of identifier used, e.g. `ENSEMBL`; read `?AnnotationDbi::columns`
`target`	Character: type of identifier to convert to; read `?AnnotationDbi::columns`
`ignoreDuplicatedTargets`	Boolean: if `TRUE`, identifiers that share targets with other identifiers will not be converted

Value

Character vector of the respective targets of gene identifiers. The previous identifiers remain other identifiers have the same target (in case ignoreDuplicatedTargets = TRUE) or if no target was found.

Examples

if ( require("org.Hs.eg.db") ) {
    columns(org.Hs.eg.db)

    genes <- c("ENSG00000012048", "ENSG00000083093", "ENSG00000141510",
               "ENSG00000051180")
    convertGeneIdentifiers(org.Hs.eg.db, genes,
                           key="ENSEMBL", target="SYMBOL")
}

[Package psichomics version 1.8.2 Index]