R/probe_exclusion.R

In NACHO: NanoString Quality Control Dashboard

#' probe_exclusion
#'
#' @param control_genes_df [[data.frame]] A `data.frame` with the count data.
#'
#' @keywords internal
#' @usage NULL
#' @noRd
#'
#' @return [[character]]
probe_exclusion <- function(control_genes_df) {
  CodeClass <- NULL # no visible binding for global variable
  local_neg <- as.matrix(
    control_genes_df[
      CodeClass %in% "Negative",
      .SD,
      .SDcols = -"CodeClass"
    ],
    "Name"
  )

  overal_median <- stats::median(local_neg)
  medians <- apply(X = local_neg, MARGIN = 1, FUN = stats::median)
  delta_medians <- sapply(medians, function(x) abs((overal_median - x)))
  ex_probes <- delta_medians[delta_medians > (0.5 * overal_median)]
  if (length(ex_probes) != 0 && nrow(local_neg) != length(ex_probes)) {
    names(ex_probes)
  } else {
    NULL
  }
}