filenames <- sprintf("%s,b=%s.xdr", simName, 1:B)
warnings("Could take a long time ...")
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$Sample.1
dat$c <- log(dat$c)
methTag <- "CnaStruct"
for (KK in candK) {
methTag <- sprintf("CnaStruct (Kmax=%s)", KK)
filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
pathname <- file.path(tpath, filename)
if (!file.exists(pathname) || segForce) {
pathCNAstruct <- system.file("otherMethods/CnaStruct", package="jointseg")
fileCNAstruct <- list.files(pathCNAstruct)
pathnameCNAstruct <- file.path(pathCNAstruct, fileCNAstruct)
source(pathnameCNAstruct)
res <- PSSeg(dat, method="other", segFUN=doCnaStruct, K=KK, profile=TRUE, verbose=FALSE, p = 0.5,maxk=len)
saveObject(res$prof[, "time"], file=pathname)
}
}
}
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