jointseg (version 1.0.2)

doPSCBS: Run Paired PSCBS segmentation

Description

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

Usage

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

Arguments

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.

Value

A list with a single element:

bkp

breakpoint positions

See Also

segmentByPairedPSCBS

Examples

# NOT RUN {
    ## load known real copy number regions
    affyDat <- acnr::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))
# }