inst/eval/GSE11976/02d.CBS.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$Sample.1
    stats <- c("c", "d", "log(c)")
    for(stat in stats){
        methTag <- sprintf("CBS:%s", stat)
        filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
        pathname <- file.path(bpath, filename)
        if (!file.exists(pathname) || segForce) {
            geno <- dat
            if(stat=="log(c)"){
                geno$c <- log2(geno$c)-1
                stat <- "c"
            }
            res <- PSSeg(geno, method="CBS", stat=stat, profile=TRUE, verbose=TRUE)
            print(res$prof[, "time"])
            saveObject(res, file=pathname)
        }
    }
}