focalCall: Detection genomic focal aberrations

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

Description

Detection of genomic focal copy number aberrations from high-resolution arrayCGH data or shallow-Seq copy number data.

Usage

	focalCall(CGHset, CNVset , focalSize = 3, minFreq=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 focalCall. Sets max size of a focal aberration/
minFreq	Threshold for the function focalCall. Sets minimal number of samples that contain the aberration/

Details

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

Value

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.

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

# 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)

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