Nothing
library(R.utils);
if (FALSE) {
## Define CN regions:
## source("05.defineCopyNumberSegments.R")
source("trunk/inst/testScripts/system/preprocessing/GSE29172/05.defineCopyNumberSegments.R")
str(regDat)
}
regPath <- "cnRegionData";
regPath <- Arguments$getReadablePath(regPath);
dataSet <- "GSE13372,ASCRMAv2"
chipType <- "GenomeWideSNP_6"
path <- file.path(regPath, dataSet, chipType);
path <- Arguments$getReadablePath(path);
sampleName <- "HCC1143_GLEYSvsHCC1143BL_GLEYS"
pattern <- sprintf("%s,([0-9]+),\\(([0-9]),([0-9])\\).rds", sampleName)
filenames <- list.files(path, pattern=pattern)
pcts <- unique(gsub(pattern, "\\1", filenames))
savPath <- file.path("extdata", "GSE13372", chipType)
savPath <- Arguments$getWritablePath(savPath);
types <- regDat[["type"]]
for (pct in pcts) {
print(pct)
pattern <- sprintf("%s,%s,(.*).rds",sampleName, pct)
filenames <- list.files(path, pattern=pattern)
types <- gsub(pattern, "\\1", filenames)
pathnames <- file.path(path, filenames)
names(pathnames) <- types
datList <- lapply(pathnames, readRDS)
dat <- NULL
for (dd in names(datList)) {
datDD <- datList[[dd]]
datDD$region <- dd
dat <- rbind(dat, datDD)
}
str(dat)
rownames(dat) <- NULL
filename <- sprintf("%s,%s,%s,cnRegions.rds", dataSet, sampleName, pct)
pathname <- file.path(savPath, filename)
saveRDS(dat, file=pathname)
}
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