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.

### See Also

Other functions for gene expression pre-processing: `filterGeneExpr()`, `normaliseGeneExpression()`, `plotGeneExprPerSample()`, `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")
    }

[Package psichomics version 1.12.1 Index]