R/filter_functions.R

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

#' keep_all_probes: return the index for each probe on an ExpressionSet
#'
#' @param   gset  An \code{ExpressionSet}.
#' @importClassesFrom   Biobase   ExpressionSet
#' @export

keep_all_probes <- function(gset) {
  stopifnot(is(gset, "ExpressionSet"))
  stopifnot(nrow(gset) > 0 && ncol(gset) > 0)
  seq_len(nrow(gset))
}

#' keep_all_entrez_probes
#'
#' @inheritParams   keep_all_probes
#' @importFrom   Biobase   featureData
#' @export

keep_all_entrez_probes <- function(gset) {
  stopifnot(is(gset, "ExpressionSet"))
  stopifnot(nrow(gset) > 0 && ncol(gset) > 0)
  stopifnot("entrez.id" %in% colnames(Biobase::featureData(gset)))
  features <- Biobase::featureData(gset)
  which(
    !is.na(features$entrez.id) & features$entrez.id != ""
  )
}

#' keep_all_samples
#'
#' @inheritParams   keep_all_probes
#' @importClassesFrom   Biobase   ExpressionSet
#' @export

keep_all_samples <- function(gset) {
  stopifnot(is(gset, "ExpressionSet"))
  stopifnot(nrow(gset) > 0 && ncol(gset) > 0)
  seq_len(ncol(gset))
}

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