inst/eval/GSE11976/02e.PSCBS.R

In mpierrejean/jointseg: Joint Segmentation of Multivariate (Copy Number) Signals

filenames <- sprintf("%s,b=%s.xdr", simName, 1:B)
for (bb in 1:B) {
    filename <- filenames[bb]
    print(filename)
    pathname <- file.path(spath, filename)
    sim <- loadObject(pathname)
    if (!is.na(normFrac)) {
        dat <- setNormalContamination(sim$profile, normFrac)
    } else {
        dat <- sim$profile
    }
    ## drop outliers
    CNA.object <- CNA(dat$c,rep(1,len),1:len)
    smoothed.CNA.obj <- smooth.CNA(CNA.object)
    dat$c <- smoothed.CNA.obj$Sample.1

    methTag <- "PSCBS"
    filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
    pathname <- file.path(bpath, filename)
    if (!file.exists(pathname) || segForce) {
        res <- PSSeg(dat, method="PSCBS", profile=FALSE, verbose=TRUE)
        print(res$prof[, "time"])
        saveObject(res, file=pathname)
    }
}