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)
}
}
}
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