focalCall (version 1.6.0)

FreqPlotfocal: frequency plot focal copy number aberrations.

Description

Frequency plot of focal aberrations in the dataset.

Usage

FreqPlotfocal(calls, header)

Arguments

calls

Object of class focalCall, contains focalCall output.

header

String with header name of frequencyPlot.

Value

A single plot is returned with the frequency of focal aberrations in the complete dataset. The x-axis represents the chromosomes, the y-axis the percentage of samples with a focal gain or focal loss at that genomic position. CNVs are also plotted but in grey.

Details

FreqPlot is applied to the calls of an object of class cghCall (as returned by focalCall version 0.0.99 or higher).

References

Krijgsman O., Benner C., Meijer G.A., Van de Wiel, M.A., Ylstra, B. (2013), "FocalCall: an R-package to detect genomic focal aberrations.", Submitted

See Also

focalCall, CGHcall

Examples

# Load example data
data(BierkensCNA)

# generate frequency plot of copy number data for focal aberrations only
FreqPlotfocal(calls_focals, "FrequencyPlot_focals_BierkensSamples")