Nothing
library("tmle.npvi")
log <- Arguments$getVerbose(-8, timestamp=TRUE)
dataSet <- "tcga2012brca"
path <- file.path("geneData", dataSet)
path <- Arguments$getReadablePath(path)
files <- list.files(path)
nas <- sapply(files, function(ff) {
obs <- loadObject(file.path(path, ff))
sum(is.na(obs))
})
files <- files[which(nas==0)]
descr <- list(thresh=2e-2,
f=identity,
flavor="learning",
nodes=1, ##3,
iter=10,
cvControl=2,
stoppingCriteria=list(mic = 0.001, div = 0.001, psi = 0.01),
nMax=30)
fileout <- sprintf("%s,tmle.npvi,%s,2014-11-21.rda", dataSet, descr$flavor)
mc.cores <- 3
nms <- unlist(strsplit(files, split=".xdr"))
TMLE <- parallel::mclapply(seq(along=files), mc.cores=mc.cores, FUN=function(ii) {
ff <- files[ii]
## loading the data
print(ii)
print(ff)
pathname <- file.path(path, ff)
obs <- loadObject(pathname)
nbcov <- ncol(extractW(obs))
if (nbcov==1) {
colnames(obs) <- c("Y", "X", "W")
}
## thresholding copy number data
whichSmall <- which(abs(obs[, "X"]) <= descr$thresh)
obs[whichSmall, "X"] <- 0
##
tmle <- try(tmle.npvi(obs=obs, f=descr$f, flavor=descr$flavor,
stoppingCriteria=descr$stoppingCriteria,
cvControl=descr$cvControl, nMax=descr$nMax))
if (inherits(tmle, "try-error")) {
return(attr(tmle, "condition"))
} else {
return(list(nbcov=nbcov, hist=getHistory(tmle)))
}
})
names(TMLE) <- nms
save(descr, TMLE, file=fileout)
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