focalCall (version 1.6.0)

singleSample: Detection focal aberrations with 1 sample only

Description

Detection and plotting of focal aberrations and distinguish somatic from germ-line in a single sample. This function, as focalCall can be used for samples with and without patient matched normal data.

Usage

singleSample(CGHset, CNVset, focalSize=3, OverlapPerc=0.2)

Arguments

CGHset

Object of class cghCall, contains CGHcall output of tumor data.

CNVset

Object of class cghCall, contains CGHcall output of matched normal data or .bed file with CNV locations.

focalSize

Threshold for the function singleSample. Sets max size of a focal aberration/

OverlapPerc

Threshold for the function singleSample. sets minimal overlap of focal aberration with CNVs from in CNdata.normal to be classified as germ-line./

Value

Three files are returned - an object of class cghCall, a text files with all focal aberrations listed and a plot with the genomic aberrations in the sample.

• "focalCall_sampleName.Rdata" is an object of class cghCall and contains all DNA copy number information including the focal aberrations.
• "focalList_sampleName.txt" is a text file with all focal aberrations detected in the sample.
• "sampleName.png" is a plot with the genomic aberrations in the sample.

Details

singleSample is applied to the calls of an object of class cghCall.

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

# generate object of cghCall class object and input files
data(BierkensCNA)

# Extract focal aberrations and distinguish somatic from germ-line copy number aberrations (CNA) in a single sample
singleSample(CGHset[,1], CNVset, focalSize=3)