Validate qsvPCs is a prcomp object

LieberInstitute · Jan 12, 2024 · c11276f · c11276f
1 parent 67113ab
commit c11276f
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Showing 2 changed files with 15 additions and 6 deletions.
diff --git a/R/get_qsvs.R b/R/get_qsvs.R
@@ -16,11 +16,16 @@
 #' get_qsvs(qsv, 2)
 get_qsvs <- function(qsvPCs, k) {
     # check that k isn't zero
-    if (k <= 0 | k > ncol(qsvPCs$x)) {
-        stop(paste("k must between 1 and",ncol(qsvPCs$x)))
-    }
+  if (k <= 0 | k > ncol(qsvPCs$x)) {
+    stop(paste("k must between 1 and",ncol(qsvPCs$x)))
+  }
 
-    qSVs <- qsvPCs$x[, seq_len(k), drop = FALSE]
-    colnames(qSVs) <- paste0("qSV", seq_len(k))
-    return(qSVs)
+  # Validate qsvPCs is a prcomp object
+  if (!is(qsvPCs, "prcomp")) {
+    stop("qsvPCs must be a prcomp object.", call. = FALSE)
+  }
+
+  qSVs <- qsvPCs$x[, seq_len(k), drop = FALSE]
+  colnames(qSVs) <- paste0("qSV", seq_len(k))
+  return(qSVs)
 }
diff --git a/tests/testthat/test-get_qsvs.R b/tests/testthat/test-get_qsvs.R
@@ -29,4 +29,8 @@ test_that("k is 0 throws an error", {
 test_that("k is higher than the number of columns throws an error", {
   k = ncol(qsv$x) + 1000
   expect_error(get_qsvs(qsv, k), paste("k must between 1 and",ncol(qsv$x)))
+})
+
+test_that("input has to be a prcomp", {
+  expect_error(get_qsvs(covComb_tx_deg, 3), "qsvPCs must be a prcomp object.")
 })