bpPlot,CopyNumberBreakPoints-method {GeneBreak} | R Documentation

## bpPlot

### Description

Plots breakpoint frequencies per chromosome

### Usage

    ## S4 method for signature 'CopyNumberBreakPoints'
    bpPlot(object, plot.chr = NULL,
      plot.ylim = 15, fdr.threshold = 0.1, add.jitter = FALSE)

### Arguments

`object` | An object of class CopyNumberBreakPoints or CopyNumberBreakPointGenes
`plot.chr` | A vector with chromosome(s) to plot. All chromosomes will be plotted when NULL is used.
`plot.ylim` | An integer giving the max y coordinate.
`fdr.threshold` | The FDR threshold to label recurrent breakpoint genes with their gene name
`add.jitter` | Logical. If TRUE, function jitter will be used for the y position of gene labels

### Details

The plot includes breakpoint locations and breakpoint gene frequencies. Genes that are recurrently affected are labeled with their gene name.

### Value

calls plot function

### Examples

    data( copynumber.data.chr20 )
    data( ens.gene.ann.hg18 )
    bp <- getBreakpoints( copynumber.data.chr20 )
    bp <- bpFilter( bp )
    bp <- addGeneAnnotation( bp, ens.gene.ann.hg18 )
    bp <- bpGenes( bp )
    bp <- bpStats( bp )

    bpPlot( bp, c(20) )

[Package GeneBreak version 1.22.0 Index]