R/downloadAndPrepareMetadata.R

In AEBilgrau/DLBCLdata: Automated and reproducible download and preprocessing of DLBCL data

#' Download GEO metadata
#'
#' Function for downloading the metadata of a GEO dataset and prepare it for
#' analysis.
#' The function uses \code{getGEOSuppFiles} which downloads the data. The
#' function then unzips the data files in the GEO series.
#'
#' @param geo_nbr The GEO ascession number.
#' @param destdir The destination dir of the downloaded files.
#' @param clean Should the strictly unnessesary files be deleted?
#' @param verbose Signal the process.
#' @return A \code{list} of \code{data.frame}s giving the clinical and metadata
#'   information for the GEO dataset.
#' @note The function will overwrite existing files in the \code{destdir}.
#' @author
#'   Anders Ellern Bilgrau,
#'   Steffen Falgreen Larsen
#' @examples
#' \dontrun{
#' print(DLBCL_overview)
#' geo_nbr <- DLBCL_overview[6,1]
#' downloadAndPrepareMetadata(geo_nbr = geo_nbr, destdir = getwd())
#' }
#' @importFrom GEOquery getGEO
#' @importFrom Biobase pData
#' @keywords internal
#' @export
downloadAndPrepareMetadata <- function(geo_nbr,
                                       destdir = getwd(),
                                       clean = FALSE,
                                       verbose = TRUE) {
  if (verbose) message("Preparing ", geo_nbr, " metadata")

  # Download data if not already downloaded
  if (verbose) message("Downloading files...")
  dl_dir <- file.path(destdir, geo_nbr)
  dir.create(dl_dir, showWarnings = FALSE, recursive = TRUE)
  dl <- getGEO(GEO = geo_nbr, destdir = dl_dir,
               GSEMatrix = TRUE, getGPL = FALSE)

  # Extract pheno data
  if (!is.list(dl)) {

    pd <- pData(dl)

  } else {

    pd <- lapply(dl, pData)

    # Merge the dataframes (if multiple)
    merge2 <- function(x, y) {
      merge(x, y, all = TRUE, sort = FALSE)
    }
    pd <- Reduce(merge2, pd)

  }

  # Set class
  class(pd) <- c(geo_nbr, class(pd))

  # Clean-up if wanted
  if (clean) {
    if (verbose) message("Removing unnessary files...")
    file.remove(file.path(destdir, geo_nbr, names(dl)))
  }

  if (verbose) message("Done.")
  return(invisible(pd))
}