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$Sample.1
stats <- list(c("log(c)","d"), "log(c)", "d")
lapply(stats, function(stat) {
for (KK in candK) {
methTag <- sprintf("GFLars+DP:%s (Kmax=%s)", paste(stat, collapse=","), KK)
filename <- sprintf("%s,b=%s,%s.xdr", simNameNF, bb, methTag)
pathname <- file.path(bpath, filename)
if (!file.exists(pathname) || segForce) {
geno <- dat
if(length(grep("log", stat))){
geno$c <- log2(geno$c)-1;
stat <- gsub("log\\(c\\)", "c", stat)
}
## drop NA or -Inf
geno$c[which(geno$c==-Inf)] <- NA
indNA <- which(is.na(geno$c))
posNotNa <- which(!is.na(geno$c))
res <- PSSeg(geno, method="GFLars", K=KK, stat=stat, profile=TRUE, verbose=FALSE)
print(res$prof[, "time"])
saveObject(res, file=pathname)
}
}
})
}
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