Fix unit test and error message for mixed annotation rownames

Co-authored-by: Nick Eagles <[email protected]>
LieberInstitute · Jan 11, 2024 · 08b5a84 · 08b5a84
1 parent 060a2b9
commit 08b5a84
Show file tree

Hide file tree

Showing 2 changed files with 13 additions and 2 deletions.
diff --git a/R/getDegTx.R b/R/getDegTx.R
@@ -57,7 +57,7 @@ getDegTx <- function(rse_tx, type = c("cell_component", "standard", "top1500"),
   is_ensembl = all(grepl("^ENST", rownames(rse_tx)) & !grepl("\\.", rownames(rse_tx)))
   if (is_ensembl) {
     sig_transcripts <- gsub("\\..*", "", sig_transcripts)
-  } else(!is_gencode) {
+  } else if (!is_gencode) {
     stop("Rownames must all be ENSEMBL or GENCODE transcript IDs.")
   }
 

diff --git a/tests/testthat/test-getDegTx.R b/tests/testthat/test-getDegTx.R
@@ -66,4 +66,15 @@ test_that("getDegTx works with original and altered row names", {
   expect_identical(original_results, altered_results)
 })
 
-
+# Test where we have mixed row names annotations (ENST and ENST.*?\.)
+test_that("Mixed row names annotations throw an error", {
+  # 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] <- "ENST00000442987" # Change the first rowname 
+  rownames(altered_covComb_tx_deg)[2] <- "ENST00000623083" # Change the second rowname 
+  expect_error({
+    # Check if mixed row names annotations (ENST and ENST.*?\.) throw an error
+    getDegTx(altered_covComb_tx_deg)
+
+  }, "Rownames must all be ENSEMBL or GENCODE transcript IDs.")
+})