CGHbase (version 1.32.0)

summaryPlot: Visualization of aCGH profiles.

Description

This function creates a summary plot for aCGH profiles.

Usage

summaryPlot(x,main='Summary Plot', gaincol='blue', losscol='red', misscol=NA, build='GRCh37', ...)

Arguments

x

An object of class cghCall.

main

Title of plot

gaincol

Color to use for gains

losscol

Color to use for losses

misscol

Missings

build

Build of Humane Genome.Either GRCh37, GRCh36, GRCh35 or GRCh34

...

Arguments plot.

Value

This function creates a plot.

Details

We find plotted on the x-axis the array probes sorted by chromosomal position. The vertical bars represent the average probability that the positions they cover are gained (green bars) or lost (red bars). The green bars represent gains, the red bars represent losses.

References

Mark A. van de Wiel, Kyung In Kim, Sjoerd J. Vosse, Wessel N. van Wieringen, Saskia M. Wilting and Bauke Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23, 892-894.

Examples

	 ## Not run: 
#   data(Wilting)
#    rawcgh <- make_cghSeg(Wilting)
#    normalized <- normalize(rawcgh)
#    segmented <- segmentData(normalized)
#    called <- CGHcall(segmented,cellularity= rep(0.75, 3))
#    summaryPlot(called)
#    ## End(Not run)