#' Download raw files from GEO for a given study
#' Example: Download the raw files of GSE11761 study and save them in a
#' directory named GSE11761 in the working directory
#'
#' @param x a GEO Series id (GSE)
#' @param y the path to save the downloaded files. By default this value is set to the working directory
#' @return downloadRaw creates a directory in the given path with the GSE name and saves there the compressed RAW files.
#' @examples \dontrun{
#' downloadRaw("GSE11761",getwd()) }
#'
#' @export
#' @importFrom GEOquery getGEOSuppFiles
downloadRaw <- function(x,y=getwd()) {
if (missing(x))
stop("Need to specify a GEO Series id, i.e 'GSE10026'")
if ( (missing(y)) | (!file.exists(y)) )
stop("Need to specify a valid path, i.e getwd()")
if (!grepl("GSE[0-9]+",x))
stop("x must be a GEO Series id, i.e 'GSE10026'")
raw <- NULL
a <- TRUE
while(a) {
raw <- try(GEOquery::getGEOSuppFiles(x, baseDir =y))
if(!inherits(raw,"try-error")) a <- FALSE
else cat("NCBI was busy, trying again\n")
}
}
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