convertGeneIdentifiers: Convert gene identifiers

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

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.

See Also

Other functions for gene expression pre-processing: filterGeneExpr(), normaliseGeneExpression(), plotGeneExprPerSample(), plotLibrarySize(), plotRowStats()

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")
}

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.