addGeneAnnotation,CopyNumberBreakPoints-method {GeneBreak} | R Documentation

## addGeneAnnotation

### Description

Maps features to gene locations.

### Usage

    ## S4 method for signature 'CopyNumberBreakPoints'
    addGeneAnnotation(object, geneAnnotation)

### Arguments

`object` | An object of class CopyNumberBreakPoints
`geneAnnotation` | An object of class `GRanges` or dataframe with at least four columns ("Gene", "Chromosome", "Start", "End")

### Details

The end of the first feature after gene start location up to and including the first feature after gene end location will be defined as gene-associated feaures. For hg18, hg19 and hg38 built-in gene annotation files obtained from ensembl can be used. Please take care to use a matching reference genome for your breakpoint data. In stead of using the built-in gene annotion files, feature-to-gene mapping can be based on an user-defined annotion file. The dataframe should contain at least these four columns: "Gene", "Chromosome", "Start" and "End".

### Value

Returns an object of class CopyNumberBreakPointGenes with gene annotation added.

### Examples

    data( copynumber.data.chr20 )
    data( ens.gene.ann.hg18 )

    ## other buil-in gene annotations are:
    # data( ens.gene.ann.hg19 )
    # data( ens.gene.ann.hg38 )

    bp <- getBreakpoints( copynumber.data.chr20 )
    bp <- bpFilter( bp )
    # input copynumber.data.chr20 is hg18 based
    bp <- addGeneAnnotation( bp, ens.gene.ann.hg18 )

    ## options to inspect the data
    bp
    accessOptions( bp )

[Package GeneBreak version 1.16.0 Index]