Add unit test to throw an error if assayname is in assayNames

LieberInstitute · Jan 12, 2024 · 4e7323b · 4e7323b
1 parent 4c86f4b
commit 4e7323b
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Showing 2 changed files with 33 additions and 22 deletions.
diff --git a/R/k_qsvs.R b/R/k_qsvs.R
@@ -27,27 +27,33 @@
 #' set.seed(20230621)
 #' k_qsvs(covComb_tx_deg, mod, "tpm")
 k_qsvs <- function(rse_tx, mod, assayname) {
-    if (qr(mod)$rank != ncol(mod)) {
-        stop("The 'mod' matrix is not full rank.", call. = FALSE)
+
+  # Check if assayname is in assayNames
+  if (!assayname %in% assayNames(rse_tx)) {
+    stop(sprintf("'%s' is not in assayNames(rse_tx).", assayname), call. = FALSE)
+  }
+
+  if (qr(mod)$rank != ncol(mod)) {
+    stop("The 'mod' matrix is not full rank.", call. = FALSE)
+  }
+  if (nrow(mod) != ncol(rse_tx)) {
+    stop("The number of rows in 'mod' does not match the number of input 'rse_tx' columns.", call. = FALSE)
+  }
+
+  expr <- log2(assays(rse_tx)[[assayname]] + 1)
+  k <- tryCatch(
+    num.sv(expr, mod),
+    error = function(e) {
+
+      if (grepl("only 0's may be mixed with negative subscripts", e$message)) {
+        warning("Could not run sva::num.sv(). Likely due to transcripts being not expressed in most samples.", call. = FALSE)
+      } else if (grepl("system is computationally singular", e$message)) {
+        warning("Could not run sva::num.sv(). Likely due to having highly correlated variables in your 'mod'.", call. = FALSE)
+      } else {
+        warning("Could not run sva::num.sv().", call. = FALSE)
+      }
+      stop(e)
     }
-    if (nrow(mod) != ncol(rse_tx)) {
-        stop("The number of rows in 'mod' does not match the number of input 'rse_tx' columns.", call. = FALSE)
-    }
-
-    expr <- log2(assays(rse_tx)[[assayname]] + 1)
-    k <- tryCatch(
-        num.sv(expr, mod),
-        error = function(e) {
-
-            if (grepl("only 0's may be mixed with negative subscripts", e$message)) {
-                warning("Could not run sva::num.sv(). Likely due to transcripts being not expressed in most samples.", call. = FALSE)
-            } else if (grepl("system is computationally singular", e$message)) {
-                warning("Could not run sva::num.sv(). Likely due to having highly correlated variables in your 'mod'.", call. = FALSE)
-            } else {
-                warning("Could not run sva::num.sv().", call. = FALSE)
-            }
-            stop(e)
-        }
-    )
-    return(k)
+  )
+  return(k)
 }
diff --git a/tests/testthat/test-k_qsvs.R b/tests/testthat/test-k_qsvs.R
@@ -43,3 +43,8 @@ test_that("test that full rank matrix works correctly", {
     # expect_warning(k_qsvs(rse_tx_low, mod, "tpm"), "Likely due to transcripts being not expressed in most samples")
     expect_silent(k_qsvs(covComb_tx_deg, mod, "tpm"))
 })
+
+# Test for assayname not in assayNames
+test_that("k_qsvs throws an error when assayname is not in assayNames", {
+  expect_error(k_qsvs(covComb_tx_deg, assayname = "not_in_assayNames"), "'not_in_assayNames' is not in assayNames\\(rse_tx\\).")
+})