Nothing
library(argparse)
suppressPackageStartupMessages(library(RnBeads))
ap <- ArgumentParser()
ap$add_argument("-x", "--xml", action="store", help="Configuration xml file")
ap$add_argument("-o", "--output", action="store", help="Output directory")
ap$add_argument("-c", "--cores", action="store", type="integer", default=1, help="Number of cores used for the analysis")
cmdArgs <- ap$parse_args()
module.name <- "import"
logger.start(fname=NA)
logger.status(c("...Started module:",module.name))
logger.start("Configuring Analysis")
rnb.settings <- rnb.xml2options(cmdArgs$xml,return.full.structure=TRUE)
data.source <- rnb.settings$analysis.params[["data.source"]]
data.type <- rnb.settings$analysis.params[["data.type"]]
report.dir <- rnb.settings$analysis.params[["dir.reports"]]
analysis.options <- rnb.settings$options
if ("preanalysis.script" %in% names(rnb.settings)){
source(rnb.settings$preanalysis.script)
}
## Set options
if (length(analysis.options) != 0) {
do.call(rnb.options, analysis.options)
}
logger.machine.name()
if (cmdArgs$cores > 1) {
parallel.setup(cmdArgs$cores)
}
aname <- rnb.getOption("analysis.name")
if (!(is.null(aname) || is.na(aname) || nchar(aname) == 0)) {
logger.info(c("Analysis Title:", aname))
}
ncores <- parallel.getNumWorkers()
if (ncores == -1) {
ncores <- 1L
}
logger.info(c("Number of cores:", ncores))
rm(aname, ncores)
logger.completed()
logger.start(fname=c(file.path(report.dir,paste0("analysis_",module.name,".log")),NA))
################################################################################
# main script
################################################################################
if (rnb.getOption("import")) {
if (is.character(data.source) || is.list(data.source) || inherits(data.source, "RnBSet")) {
result <- rnb.run.import(data.source, data.type, report.dir)
rnb.set <- result$rnb.set
} else {
stop("invalid value for data.source")
}
} else if (inherits(data.source, "RnBSet")) {
rnb.set <- data.source
} else if (inherits(data.source, "MethyLumiSet")) {
rnb.set <- as(data.source, "RnBeadSet")
} else {
logger.warning("Cannot proceed with the supplied data.source. Check the option import")
logger.completed()
if (!is.null(logfile)) {
logger.close()
}
}
RnBeads:::rnb.cleanMem()
logger.start("Saving")
save.rnb.set(rnb.set, file.path(cmdArgs$output,paste0(module.name,"_RnBSet")), archive=FALSE)
logger.completed()
logger.status(c("...Completed module:",module.name))
quit(save='no')
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.