segPlot: CNomplexity::segPlot

In SteeleCD/CNomplexity: Analysis of Complex Copy Cumber and Structural Variants in Cancer Genomes.

Description

Function to plot a segment profile., with options to higlight some regions, and plot vertical bars at fusion positions.

Usage

segPlot(segFile=NULL,segObj=NULL,dataDir,
		outDir=NULL,fileName=NULL,
		sampleCol=2,chromCol=1,startCol=3,endCol=4,nMarkCol=NULL,segMeanCol=6,
		plotAber=FALSE,highlightChroms=NULL,highlightStarts=NULL,highlightEnds=NULL,
		fusionChroms=NULL,fusionPos=NULL,segColour=NULL)

Arguments

segFile	Segment file to plot.
segObj	Segment object to plot.
dataDir	Data directory if segFile!=NULL.
outDir	Out directory for plotting.
fileName	OUt filename for plotting.
sampleCol	Sample column of seg profile.
chromCol	Chromsome column of seg profile.
startCol	Start column of seg profile.
endCol	End column of seg profile.
nMarkCol	Seg column with number of markers.
segMeanCol	Seg column with copy number.
highlightChroms	Chromsomes of regions to highlight.
highlightStarts	Start positions of regions to highlight.
highlightEnds	End positions of regions to highlight.
fusionChroms	Chromosomes of fusions to plot.
fusionPos	Positions of fusions to plot.
segColour	Colour for segments.

Details

Plots a segment profile, with options to higlight some regions, and plot vertical bars at fusion positions.

Value

NULL

SteeleCD/CNomplexity documentation built on May 29, 2019, 2:09 p.m.