From ef5c79b0cf952db41cf2224a9fe9b5e631c877ff Mon Sep 17 00:00:00 2001
From: HediaTnani <hediatnani0@gmail.com>
Date: Wed, 3 Jan 2024 17:02:30 -0500
Subject: [PATCH] Use arg_match for type in case user provide invalid type
 name. Better error message for rse object.

---
 NAMESPACE       |  1 +
 R/getDegTx.R    | 20 ++++++++++++++------
 man/getDegTx.Rd |  2 +-
 3 files changed, 16 insertions(+), 7 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 9bdfe86..347bb19 100644
--- a/NAMESPACE
+++ b/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)
diff --git a/R/getDegTx.R b/R/getDegTx.R
index 9104349..108bd27 100644
--- a/R/getDegTx.R
+++ b/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)
 }
diff --git a/man/getDegTx.Rd b/man/getDegTx.Rd
index 5ac0e48..2765b17 100644
--- a/man/getDegTx.Rd
+++ b/man/getDegTx.Rd
@@ -6,7 +6,7 @@
 \usage{
 getDegTx(
   rse_tx,
-  type = "cell_component",
+  type = c("cell_component", "standard", "top1500"),
   sig_transcripts = select_transcripts(type),
   assayname = "tpm"
 )