plotCompiledCNV {exomeCopy} | R Documentation |
This function takes a GRanges object as produced by
compileCopyCountSegments
and plots the CNV segments for
one sequence/chromosomes across the samples with CNV segments.
The segments in the normal state should be removed as shown below in the example to produce a cleaned GRanges object. See the vignette for a more complete example.
plotCompiledCNV(CNV.segments, seq.name, xlim=NULL, col=NULL, copy.counts=0:6, normal.state = 2)
CNV.segments |
A GRanges object as produced by
|
seq.name |
The name of the sequence to plot |
xlim |
The genomic coordinates for the x axis. If not included, the
plotting window will cover the range of the CNVs in |
col |
The colors to use for the different copy count states |
copy.counts |
The corresponding copy counts for the colors |
normal.state |
The copy count of the normal state |
Produces a plot.
example(compileCopyCountSegments) CNV.clean <- CNV.segments[CNV.segments$copy.count != 2] chr.start <- start(range(fit@ranges)) chr.end <- end(range(fit@ranges)) plotCompiledCNV(CNV.clean, "chr1", xlim=c(chr.start,chr.end))