bpPlot-CopyNumberBreakPoints-method: bpPlot
In GeneBreak: Gene Break Detection

Description Usage Arguments Details Value Examples

Plots breakpoint frequencies per chromosome

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

`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

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

calls plot function

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) )