focalCall {focalCall} | R Documentation |
Detection of genomic focal copy number aberrations from high-resolution arrayCGH data or shallow-Seq copy number data.
focalCall(CGHset, CNVset , focalSize = 3, minFreq=2)
CGHset |
Object of class |
CNVset |
Object of class |
focalSize |
Threshold for the function |
minFreq |
Threshold for the function |
focalCall is applied to the calls of an object of class cghCall
(as returned by CGHcall version 1.2.0 or higher). FocalCall extract all focal aberrations from the tumor copy number data and
Two files are returned - an object of class cghCall
and a text files with all focal aberrations detected in all sample.
"focalCall.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 set of 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) ExampleRun<-focalCall(CGHset, CNVset, focalSize=3, minFreq=2)