singleSample {focalCall} | R Documentation |
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.
singleSample(CGHset, CNVset, focalSize=3, OverlapPerc=0.2)
CGHset |
Object of class |
CNVset |
Object of class |
focalSize |
Threshold for the function |
OverlapPerc |
Threshold for the function |
singleSample is applied to the calls of an object of class cghCall
.
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.
Oscar Krijgsman: o.krijgsman@vumc.nl
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
focalCall
, CGHcall
# 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)