doPSCBS: Run Paired PSCBS segmentation
In jointseg: Joint segmentation of multivariate (copy number) signals

Description Usage Arguments Value Author(s) See Also Examples

This function is a wrapper for convenient use of the PSCBS segmentation method by PSSeg. It applies the segmentByPairedPSCBS function and reshapes the results

1	doPSCBS(Y, ..., verbose = FALSE)

Y

A matrix of signals to be segmented, containing the following columns

c: total copy numbers
b: allele B fractions (a.k.a. BAF)
genotype: germline genotypes

...

Arguments to be passed to segmentByPairedPSCBS

verbose

A logical value: should extra information be output ? Defaults to FALSE.

bkp

breakpoint positions

Morgane Pierre-Jean and Pierre Neuvial

segmentByPairedPSCBS

if (require("PSCBS") && require("aroma.light")) {
    ## load known real copy number regions
    affyDat <- loadCnRegionData(dataSet="GSE29172", tumorFraction=1)
    
    ## generate a synthetic CN profile
    K <- 10
    len <- 1e4
    sim <- getCopyNumberDataByResampling(len, K, minLength=100, regData=affyDat)
    datS <- sim$profile
    
    ## run PSCBS segmentation
    Y <- as.matrix(subset(datS, select=c(c, b, genotype)))
    res <- doPSCBS(Y)
    getTpFp(res$bkp, sim$bkp, tol=5, relax = -1)   ## true and false positives
    plotSeg(datS, breakpoints=list(sim$bkp, res$bkp))
}