bpPlot,CopyNumberBreakPoints-method {GeneBreak} | R Documentation |
Plots breakpoint frequencies per chromosome
## 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) )