#' Download and process all curated DLBCL datasets

#'

#' Automatically download and process all support curated DLBCL datasets.

#' Simply loops over all datasets in \code{data(dlbcl_overview)}.

#'

#' @param \dots Arguments passed to \code{\link{downloadAndProcessGEO}}.

#' @return Saves a \code{list} of the processed datasets in the working

#'   directory named "dlbcl_data.Rds".

#'   Invisibly returns a \code{list} of the output of

#'   \code{\link{downloadAndProcessGEO}}.

#' @author

#'   Anders Ellern Bilgrau\cr

#'   Steffen Falgreen Larsen

#' @examples

#' listTargets("brainarray")

#' \dontrun{

#' # Warning, very long processing times if data is not downloaded.

#'

#' # Preprocess with brainarray "Entrez" gene ids

#' res <- downloadAndProcessDLBCL(cdf = "brainarray", target = "ENTREZG",

#'                                clean = FALSE)

#'

#' # Preprocess with brainarray "Ensembl" gene ids

#' res2 <- downloadAndProcessDLBCL(cdf = "brainarray", target = "ENSG",

#'                                 clean = TRUE)

#'

#' # Preprocess with affy's probesets

#' res3 <- downloadAndProcessDLBCL()  #= downloadAndProcessDLBCL(cdf = "affy")

#' }

#' @export

downloadAndProcessDLBCL <- function(...) {

  st <- proc.time()

  message("\nDownloading and processing all DLBCL datasets\n")

  res <- list()

  for (i in 1:nrow(DLBCLdata::DLBCL_overview)) {

    geo_nbr <- as.character(DLBCLdata::DLBCL_overview$GSE[i])

    stdy    <- as.character(DLBCLdata::DLBCL_overview$Study[i])

    message(sprintf("\n\n\n\n #### %s (%s) ####\n\n\n", geo_nbr, stdy))

    t <- system.time({

      res[[i]] <- downloadAndProcessGEO(geo_nbr = geo_nbr, ...)

    })

    message(sprintf("\n %s finished successfully in %s minutes.\n",

                    geo_nbr, t[3] %/% 60))

  }

  names(res) <- as.character(DLBCLdata::DLBCL_overview$GSE)

  message("Saving all processed DLBCL data")

  saveRDS(res, file = file.path(getwd(), "dlbcl_data.Rds"))

  message("\nFinished  in ", (proc.time()-st)[3] %/% 60, " minutes.\n")

  return(invisible(res))

}