--- a
+++ b/R/downloadAndProcessGEO.R
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+#' Download GEO dataset and preprocess it
+#'
+#' Functionality for automatically downloading, RMA preprocessing the array
+#' data and formatting the phenotype data, and saving the results in a
+#' \code{.Rds} file.
+#'
+#' @param geo_nbr The GEO ascession number.
+#' @param destdir The destination dir of the downloaded files.
+#' @param ... Arguments passed to \code{\link{preprocessCELFiles}}
+#' @param clean Should the strictly unnessesary files be deleted?
+#' @param verbose Signal the process.
+#' @return
+#'   Creates a folder with the downloaded and processed files.
+#'   The processed files are saved as an \code{.Rds} object named
+#'   after the used parameters.
+#'   Invisibly returns the saved object.
+#' @note The function will overwrite existing files in the \code{destdir}.
+#'
+#'   Arguments after \code{\dots} must be named.
+#' @author
+#'   Anders Ellern Bilgrau,
+#'   Steffen Falgreen Larsen
+#' @examples
+#' \dontrun{
+#' print(DLBCL_overview)
+#' geo_nbr <- DLBCL_overview[6,1]
+#' res <- downloadAndProcessGEO(geo_nbr = geo_nbr, cdf = "brainarray",
+#'                              target = "ENSG", clean = FALSE)
+#' head(exprs(res$es$Batch1))
+#' }
+#' @export
+downloadAndProcessGEO <- function(geo_nbr,
+                                  destdir = getwd(),
+                                  ...,
+                                  clean = FALSE,
+                                  verbose = TRUE) {
+
+  # Download metadata
+  meta_data <- downloadAndPrepareMetadata(geo_nbr = geo_nbr, destdir = destdir,
+                                          clean = clean, verbose = verbose)
+
+   # Process metadata
+  clean_meta_data <- cleanMetadata(meta_data)
+  GSM_met <- basenameSansCEL(rownames(clean_meta_data))
+  stopifnot(all(GSM_met == clean_meta_data$GSM))
+
+  # Download array data
+  cel_files <- downloadAndPrepareCELFiles(geo_nbr = geo_nbr, destdir = destdir,
+                                          clean = clean, verbose = verbose)
+  GSM_cel <- gsub("(GSM[0-9]+).*$", "\\1", basenameSansCEL(cel_files))
+
+  # Add local filenames to cleaned data
+  clean_meta_data$file <- cel_files[pmatch(GSM_met, GSM_cel)]
+
+  # Checks and warnings
+  if (!all(GSM_cel %in% GSM_met)) {
+    warning("Not all downloaded CEL files are in the metadata")
+  }
+  if (!all(GSM_met %in% GSM_cel)) {
+    warning("Not all GSM numbers in the metadata have CEL files")
+  }
+
+  # Preprocess array data by RMA for each batch
+  if (is.null(clean_meta_data$Batch)) {
+    es <- preprocessCELFiles(cel_files, ...)
+  } else {
+    if (verbose) {
+      message("Batches detected. RMA normalizing each of the batches: ",
+              paste0(unique(clean_meta_data$Batch), collapse = ", "))
+    }
+    batch_list <- with(clean_meta_data, split(file, Batch))
+    es <- lapply(batch_list, preprocessCELFiles, ...)
+  }
+
+  # Save Rds file
+  a         <- list()
+  a$cdf     <- tolower(finfo(es, "cdf"))
+  a$target  <- finfo(es, "target")
+  a$version <- finfo(es, "version")
+  file_name <-
+    paste0(geo_nbr, "_", a$cdf,
+           ifelse(a$target != "", "_", ""),
+           tolower(a$target),
+           ifelse(a$cdf == "affy", "", paste0("_", a$version)),
+           ".Rds")
+  output <- list(es = es, metadata = clean_meta_data, call = match.call())
+  saveRDS(output, file = file.path(destdir, geo_nbr, file_name))
+
+  # Clean if wanted
+  if (clean) file.remove(cel_files)
+  if (verbose) message("done.\n")
+
+  return(invisible(output))
+}
+
+finfo <- function(x, y) {
+  if (!is.list(x)) {
+    x <- list(x)
+  }
+  info <- unique(unlist(lapply(x, function(e) attributes(e)[[y]])))
+  ans <- paste(info, collapse = "-")
+  return(ans)
+}