Nothing
library("tmle.npvi")
rootPath <- "geneData"
rootPath <- Arguments$getReadablePath(rootPath)
dataSet <- "tcga2012brca"
path <- file.path(rootPath, dataSet)
path <- Arguments$getReadablePath(path)
files <- list.files(path, pattern=".*chr17,.*.xdr")
idxs <- 1:150
if (FALSE) {
files <- list.files(path, pattern=".*chr21,.*.xdr")
idxs <- seq(along=files)
}
filenames <- files[idxs]
pathnames <- file.path(path, filenames)
obsList <- lapply(pathnames, loadObject)
snames <- gsub("\\.xdr", "", filenames)
names(obsList) <- snames
str(obsList)
tcga2012brca <- obsList
save(tcga2012brca, file="tcga2012brca.rda")
if (FALSE) {
opath <- "data"
opath <- Arguments$getWritablePath(opath)
for (ff in seq(along=idxs)) {
filename <- files[ff]
pathname <- file.path(path, filename)
obs <- loadObject(pathname)
sname <- gsub("\\.xdr", "", filename)
ofilename <- sprintf("%s,%s.txt", dataSet, sname)
opathname <- file.path(opath, ofilename)
write.table(obs, opathname, quote=FALSE, row.names=FALSE)
}
}
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