Use arg_match for type in case user provide invalid type name. Better…

… error message for rse object.

NAMESPACE

@@ -9,6 +9,7 @@ export(qSVA)
 export(select_transcripts)
 import(SummarizedExperiment)
 import(ggplot2)
+import(rlang)
 importFrom(methods,is)
 importFrom(stats,cor)
 importFrom(stats,prcomp)

R/getDegTx.R

@@ -28,15 +28,23 @@
 #'
 #' @export
 #' @importFrom methods is
+#' @import rlang
 #'
 #' @examples
 #' getDegTx(covComb_tx_deg)
 #' stopifnot(mean(rowMeans(assays(covComb_tx_deg)$tpm)) > 1)
-getDegTx <- function(rse_tx, type = "cell_component", sig_transcripts = select_transcripts(type), assayname = "tpm") {
-    stopifnot(is(rse_tx, "RangedSummarizedExperiment"))
-    rse_tx <- rse_tx[rownames(rse_tx) %in% sig_transcripts, , drop = FALSE]
-    if (mean(rowMeans(assays(rse_tx)[[assayname]])) < 1) {
-        warning("The transcripts selected are lowly expressed in your dataset. This can impact downstream analysis.")
+getDegTx <- function(rse_tx, type = c("cell_component", "standard", "top1500"), sig_transcripts = select_transcripts(type), assayname = "tpm") {
+
+  type = arg_match(type)
+
+  # Validate rse_tx is a RangedSummarizedExperiment object
+  if (!is(rse_tx, "RangedSummarizedExperiment")) {
+    stop("Error: rse_tx must be a RangedSummarizedExperiment object.")
+  }
+
+  rse_tx <- rse_tx[rownames(rse_tx) %in% sig_transcripts, , drop = FALSE]
+  if (mean(rowMeans(assays(rse_tx)[[assayname]])) < 1) {
+    warning("The transcripts selected are lowly expressed in your dataset. This can impact downstream analysis.")
     }
-    return(rse_tx)
+  return(rse_tx)
 }