#' Read DLBCL class files

#'

#' Functions to read the internal data files of classified CEL files using

#' the DLBCL Automatic Classifier (DAC) [1]. These were manually supplied to the

#' DAC Windows interface.

#'

#' @param geo_nbr A \code{character} string giving the GSE number.

#' @return A \code{data.frame} of the predicted classes and the class

#'   probabilities. Returns \code{NULL} if \code{geo_nbr} is not found.

#' @author

#'   Anders Ellern Bilgrau \cr

#'   Steffen Falgreen

#' @references

#'   [1] Care, M. A., Barrans, S., Worrillow, L., Jack, A., Westhead, D. R., &

#'       Tooze, R. M. (2013). A microarray platform-independent classification

#'       tool for cell of origin class allows comparative analysis of gene

#'       expression in diffuse large B-cell lymphoma.

#'       PloS One, 8(2), e55895. doi:10.1371/journal.pone.0055895

#' @note

#' The GSE11318 dataset was not classified using the DAC.

#' @examples

#' head(DLBCL_overview[, -c(3,4,6)])

#'

#' head(readDACData("GSE19246"))

#'

#' readDACData("UNSUPPORTED_STUDY")

#' @export

readDACData <- function(geo_nbr) {

  extdir <- system.file("extdata", package = "DLBCLdata")

  files <- list.files(extdir, pattern = "^predictions-.+\\.txt$",

                      full.names = TRUE)

  file <- grep(geo_nbr, files, value = TRUE)

  dat <- lapply(file, read.table, header = TRUE)

  names(dat) <- gsub("predictions-|\\.txt$", "", basename(file))

  ans <- do.call(rbind, dat)

  return(ans)

}