Add checks and unit tests of rse_tx as an rse and mod as a matrix

Co-authored-by: Nick Eagles <nickeagles77@gmail.com>

R/k_qsvs.R

@@ -28,19 +28,33 @@
 #' k_qsvs(covComb_tx_deg, mod, "tpm")
 k_qsvs <- function(rse_tx, mod, assayname) {
 
+  # Validate rse_tx is a RangedSummarizedExperiment object
+  if (!is(rse_tx, "RangedSummarizedExperiment")) {
+    stop("'rse_tx' must be a RangedSummarizedExperiment object.", 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)
   }
 
+  # Check if mod is a matrix
+  if (!is(mod, "matrix")) {
+    stop("'mod' must be a matrix.", call. = FALSE)
+  }
+
+  # Check if mod is full rank
   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)
   }
 
+  # Get expression data normalized by log2
   expr <- log2(assays(rse_tx)[[assayname]] + 1)
+
+  # Run num.sv
   k <- tryCatch(
     num.sv(expr, mod),
     error = function(e) {

tests/testthat/test-k_qsvs.R

@@ -24,12 +24,22 @@ test_that("output is an numeric", {
     expect_equal(class(k_res), "numeric")
 })
 
+# Test for input is an rse object
+test_that("getDegTx throws an error when input is not a RangedSummarizedExperiment object", {
+  qsv <- list(x = matrix(seq_len(9), ncol = 3))
+  expect_error(getDegTx(qsv, assayname = "tpm"), "'rse_tx' must be a RangedSummarizedExperiment object.")
+})
+
+# 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\\).")
+})
+
 # Test when number of rows in 'mod' does not match number of columns in 'rse_tx'
 test_that("Number of rows in 'mod' does not match number of columns in 'rse_tx'", {
   mod_not_matching <- mod
   mod_not_matching <- mod_not_matching[-1, ]
-  expect_error(k_qsvs(covComb_tx_deg, mod_not_matching, "tpm"), 
-               "The number of rows in 'mod' does not match the number of input 'rse_tx' columns.")
+  expect_error(k_qsvs(covComb_tx_deg, mod_not_matching, "tpm"), "The number of rows in 'mod' does not match the number of input 'rse_tx' columns.")
 })
 
 test_that("non-full rank data throws error", {
@@ -44,7 +54,8 @@ test_that("test that full rank matrix works correctly", {
     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\\).")
-})
+test_that("test that mod is a matrix", {
+    set.seed(20230621)
+    expect_error(k_qsvs(covComb_tx_deg, mod = "mod", assayname = "tpm"), "'mod' must be a matrix.")
+})
+