#' RMA preprocess CEL files

#'

#' General function for RMA processing microarray data. Automatically downloads

#' custom Brainarray chip definition files (cdf) if wanted.

#'

#' @param cel_files A character vector of .CEL files.

#' @param cdf A character specifying the CDF type to use. Should be either

#'   \code{"brainarray"} or \code{"affy"}.

#' @param target Specifies the "target" CDF to use depending on \code{cdf}.

#'   If \code{cdf} is \code{"affy"} then \code{target} is e.g. \code{"core"}.

#'   If \code{cdf} is \code{"brainarray"} then \code{target} is

#'   e.g. \code{"ensg"}, \code{"entrez"}.

#'   See \code{listTargets()} to list the available targets.

#' @param version A character giving the brainarray version to be used.

#'   Only used if \code{cdf} is \code{"brainarray"}. See \code{listVersions()}.

#' @param background boolean. Should RMA background correction be performed?

#' @param normalize boolean. Should RMA normalization be performed?

#' @return An expression set object.

#' @importFrom affy read.affybatch just.rma

#' @importFrom affyio read.celfile.header

#' @importFrom oligo rma

#' @export

preprocessCELFiles <- function(cel_files,

                               cdf = c("affy", "brainarray"),

                               target,

                               version = getLatestVersion(),

                               background = TRUE,

                               normalize = TRUE) {

  getCDF <- function(file) {

    return(read.celfile.header(file)$cdfName)

  }

  array_type <- sapply(cel_files, getCDF)

  array_types <- unique(array_type)

  if (length(array_types) != 1) {

    stop("The CEL files are from more that one array platform. The unique ",

         "platforms are: ", paste(array_types, collapse = ", "),

         ". The arrays should be preprocessed in batches of array platforms.")

  }

  array_type <- array_type[1]

  cel_files <- normalizePath(cel_files)

  cdf <- match.arg(cdf)

  if (tolower(cdf) == "affy") {

    # Load expression set

    es <- oligo::read.celfiles(cel_files)

    # RMA normalize

    if (class(es) %in% c("ExonFeatureSet","HTAFeatureSet","GeneFeatureSet")) {

      if (missing(target)) stop("No target provided.")

      es_rma <- oligo::rma(es, background = background,

                           normalize = normalize, target = target)

      attr(es_rma, "target") <- target

    } else {

      es_rma <- oligo::rma(es, background = background,

                           normalize = normalize)

      attr(es_rma, "target") <- NULL

    }

  } else if (tolower(cdf) == "brainarray") {

    if (missing(target)) stop("No target provided.")

    req <- requireBrainarray(array_type = array_type,

                             custom_cdf = target,

                             version = version)

    suppressWarnings({

      es_rma <- just.rma(filenames = cel_files,

                         verbose = TRUE,

                         cdfname = getCustomCDFName(req$brain_dat, array_type))

    })

    attr(es_rma, "target") <- target

  } else {

    stop("cdf == '", cdf,

         "' not supported. Should be either 'affy' or 'brainarray'")

  }

  # Add attributes

  attr(es_rma, "cdf") <- cdf

  attr(es_rma, "version") <- version

  attr(es_rma, "background") <- background

  attr(es_rma, "normalize") <- normalize

  return(es_rma)

}