--- a
+++ b/R/rnaseq.R
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+#' Utility for using voom transformation with TMLE for biomarker discovery
+#'
+#' This function prepares next-generation sequencing data (counts) for use with
+#' the biomarker TMLE procedure by invoking the voom transform of \code{limma}.
+#'
+#' @param biotmle A \code{bioTMLE} object containing next-generation sequencing
+#'  count data in its "assays" slot.
+#' @param weights A \code{logical} indicating whether to return quality weights
+#'  of samples in the output object.
+#' @param ... Other arguments to be passed to \code{\link[limma]{voom}} or
+#'  \code{\link[limma]{voomWithQualityWeights}} as appropriate.
+#'
+#' @importFrom tibble as_tibble
+#' @importFrom limma voom voomWithQualityWeights
+#' @importFrom SummarizedExperiment assay
+#' @importFrom assertthat assert_that
+#' @importFrom methods is
+#'
+#' @export rnaseq_ic
+#'
+#' @return \code{EList} object containing voom-transformed expression measures
+#'  of count data (actually, the mean-variance trend) in the "E" slot, to be
+#'  passed into the biomarker TMLE procedure.
+rnaseq_ic <- function(biotmle, weights = TRUE, ...) {
+  # check arguments
+  assertthat::assert_that(is(biotmle, "bioTMLE"))
+  assertthat::assert_that(is.logical(weights))
+
+  # extract count data from appropriate slot of SummarizedExperiment object
+  ngs_data <- tibble::as_tibble(assay(biotmle))
+
+  # invoke the "voom" transform from LIMMA
+  if (weights) {
+    voom_data <- limma::voomWithQualityWeights(ngs_data,
+      normalize.method = "scale",
+      ...
+    )
+  } else {
+    voom_data <- limma::voom(ngs_data,
+      normalize.method = "scale",
+      ...
+    )
+  }
+  return(voom_data)
+}