GeneBreak (version 1.2.0)

bpPlot,CopyNumberBreakPoints-method: bpPlot

Description

Plots breakpoint frequencies per chromosome

Usage

"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

Value

calls plot function

Details

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

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) )