summaryPlot: Visualization of aCGH profiles.

In CGHbase: CGHbase: Base functions and classes for arrayCGH data analysis.

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.

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.

Value

This function creates a plot.

Author(s)

Sjoerd Vosse & Mark van de Wiel

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)

CGHbase documentation built on Nov. 8, 2020, 5:04 p.m.