frequencyPlotCalls {CGHbase} | R Documentation

## Visualization of aCGH profiles.

### Description

This function creates a frequency plot for aCGH profiles.

### Usage

    	frequencyPlotCalls(x,main='Frequency 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 frequency of gains or 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))
       frequencyPlotCalls(called)

    ## End(Not run)

[Package CGHbase version 1.42.0 Index]