addGeneAnnotation-CopyNumberBreakPoints-method: addGeneAnnotation

In GeneBreak: Gene Break Detection

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 )

GeneBreak documentation built on Nov. 8, 2020, 8:18 p.m.