FreqPlotfocal: frequency plot focal copy number aberrations.

In focalCall: Detection of focal aberrations in DNA copy number data

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.

Details

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

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.

Author(s)

Oscar Krijgsman: [e-mail]

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")

focalCall documentation built on April 28, 2020, 9:09 p.m.