summaryPlot {CGHbase} | R Documentation

## 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`.

### 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)

[Package CGHbase version 1.40.0 Index]