Add unit test for assayname not in assayNames in qSVA function

LieberInstitute · Jan 12, 2024 · 3dd703f · 3dd703f
1 parent c6e12f4
commit 3dd703f
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Showing 2 changed files with 13 additions and 1 deletion.
diff --git a/R/qSVA.R b/R/qSVA.R
@@ -42,7 +42,14 @@ qSVA <-
     assayname) {
         ## We don't need to pass type to getDegTx() since it's not used internally
         ## once the sig_transcripts have been defined.
-        DegTx <-
+
+      # Check if assayname is in assayNames
+      if (!assayname %in% assayNames(rse_tx)) {
+        stop(sprintf("'%s' is not in assayNames(rse_tx).", assayname), call. = FALSE)
+      }
+
+      # Get the qSVs
+      DegTx <-
             getDegTx(rse_tx, sig_transcripts = sig_transcripts, assayname = assayname)
         PCs <- getPCs(DegTx, assayname)
         k <- k_qsvs(DegTx, mod = mod, assayname = assayname)

diff --git a/tests/testthat/test-qSVA.R b/tests/testthat/test-qSVA.R
@@ -22,3 +22,8 @@ test_that("output is a matrix", {
 test_that("output is an array", {
     expect_equal(class(qsva_cc)[2], "array")
 })
+
+# Test for assayname not in assayNames
+test_that("qSVA throws an error when assayname is not in assayNames", {
+  expect_error(qSVA(covComb_tx_deg, type = "standard", mod = mod,assayname = "not_in_assayNames"), "'not_in_assayNames' is not in assayNames\\(rse_tx\\).")
+})