Fix tests after interactive debugging

tests/testthat/test-getDegTx.R

@@ -1,7 +1,10 @@
 # Filter out lowly expressed transcripts and test if the number of rows in getDegTx output matches expected transcript count
 rse_tx_low <- rse_tx[rowMeans(assays(rse_tx)$tpm) < 1, ]
 test_that("length for number of rows is the same as length sig_transcripts", {
-    expect_equal(nrow(getDegTx(rse_tx)), length(select_transcripts()))
+    expect_equal(
+        nrow(getDegTx(rse_tx)),
+        length(intersect(rownames(rse_tx), select_transcripts()))
+    )
 })
 
 # Test if number of columns in getDegTx output matches number of columns in original dataset

tests/testthat/test-qSVA.R

@@ -12,8 +12,26 @@ qsva_cc <- qSVA(
 qsva_standard <- qSVA(rse_tx = rse_tx, mod = mod, assayname = "tpm")
 
 test_that("number of qsvs is k", {
-    expect_equal(length(colnames(qsva_cc)), 10)
-    expect_equal(length(colnames(qsva_standard)), 8)
+    expect_equal(
+        ncol(qsva_cc),
+        k_qsvs(
+            rse_tx[
+                intersect(
+                    rownames(rse_tx), select_transcripts(cell_component = TRUE)
+                ),
+            ],
+            mod,
+            assayname = "tpm"
+        )
+    )
+    expect_equal(
+        ncol(qsva_cc),
+        k_qsvs(
+            rse_tx[intersect(rownames(rse_tx), select_transcripts()),],
+            mod,
+            assayname = "tpm"
+        )
+    )
 })
 
 test_that("length of qsv rownames is the same as number of samples", {

tests/testthat/test-utils.R

@@ -5,7 +5,7 @@ test_that("check_tx_names throw error if annotation is not GENCODE or ENSEMBL",
     # For testing the error condition, altered manually rownames of rse_tx
     altered_rse_tx <- rse_tx
     rownames(altered_rse_tx) <- paste0("gene", 1:length(rownames(altered_rse_tx)))
-    sig_transcripts <- select_transcripts("cell_component")
+    sig_transcripts <- select_transcripts(cell_component = TRUE)
     expect_error(which_tx_names(rownames(altered_rse_tx), sig_transcripts))
     expect_error(which_tx_names(sig_transcripts, rownames(altered_rse_tx)))
 })