R/preprocess_classes.R

In russHyde/miiq: Microarrays Are Awesome: Get Them Analysed HERE!

#' Class definition for MicroarrayPreprocessConfig
#'
#' @name         MicroarrayPreprocessConfig-class
#' @rdname       MicroarrayPreprocessConfig-class
#'
#' @exportClass   MicroarrayPreprocessConfig
#'
methods::setClass(
  Class = "MicroarrayPreprocessConfig",
  slots = list(
    acc = "character",
    annot_gpl = "logical",
    entrezgene_db = "OrgDb",
    keep_sample_fn = "function",
    keep_probe_fn = "function"
  )
)

methods::setMethod(
  f = "initialize",
  signature = methods::signature("MicroarrayPreprocessConfig"),
  definition = function(.Object, ...) {
    .Object <- methods::callNextMethod()
    .Object
  }
)

#' Sets up a class for storing the options for preprocessing ExpressionSets
#' (that is, filtering the samples and probes; adding entrez and symbol
#' columns)
#'
#' @param        acc           An identifier for the microarray dataset.
#'   Typically this would be the GEO or ArrayExpress identifier.
#' @param        entrezgene_db   A string or an \code{OrgDB} defining an
#'   entrezgene database.
#' @param        annot_gpl     Logical. Have the features in the dataset been
#'   annotated with a GPL?
#' @param        keep_sample_fn,keep_probe_fn   Functions that return a vector
#'   of integer indices that can be used to subset an ExpressionSet. By
#'   default, all samples and features will be kept. Can be specified as a
#'   function literal or a "function_name" or a "pkg_name::function_name"
#'   string. If NULL, the default functions will keep all samples or keep all
#'   probes.
#'
#' @include   filter_functions.R   utils.R
#' @export
#'
MicroarrayPreprocessConfig <- function(
                                   acc,
                                   entrezgene_db,
                                   keep_sample_fn = NULL,
                                   keep_probe_fn = NULL,
                                   annot_gpl = as.logical(NA)) {
  if (is.null(keep_sample_fn)) {
    keep_sample_fn <- keep_all_samples
  }
  if (is.null(keep_probe_fn)) {
    keep_probe_fn <- keep_all_probes
  }

  new(
    "MicroarrayPreprocessConfig",
    acc = acc,
    entrezgene_db = .get_from_env(entrezgene_db),
    keep_sample_fn = .get_from_env(keep_sample_fn),
    keep_probe_fn = .get_from_env(keep_probe_fn),
    annot_gpl = annot_gpl
  )
}

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