Add a check in the getDegTx function and an error when rownames not s…

…tarting with "ENST"

R/getDegTx.R

@@ -41,7 +41,9 @@ getDegTx <- function(rse_tx, type = c("cell_component", "standard", "top1500"),
   if (!is(rse_tx, "RangedSummarizedExperiment")) {
     stop("Error: rse_tx must be a RangedSummarizedExperiment object.")
   }
-
+  if (any(!grepl("^ENST", rownames(rse_tx)))) {
+    stop("Error: Some rownames do not start with 'ENST'.")
+  }
   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.")

tests/testthat/test-getDegTx.R

@@ -19,3 +19,17 @@ test_that("test warning output for lowly expressed transcripts", {
     expect_warning(getDegTx(rse_tx_low))
 })
 
+# Test for rownames starting with "ENST"
+test_that("getDegTx correctly processes covComb_tx_deg", {
+  # If covComb_tx_deg is correctly structured and all rownames start with "ENST", expect no error
+  expect_silent(getDegTx(covComb_tx_deg))
+  # For testing the error condition, altered manually rownames of covComb_tx_deg
+  altered_covComb_tx_deg <- covComb_tx_deg
+  rownames(altered_covComb_tx_deg)[1] <- "INVALID0001" # Change the first rowname to an invalid one
+
+  # Expect an error when rownames do not start with "ENST"
+  expect_error(getDegTx(altered_covComb_tx_deg), "Error: Some rownames do not start with 'ENST'.")
+})
+
+
+