From c11276fecaaaf2ad41f8ce86cf1c40247ccc8825 Mon Sep 17 00:00:00 2001
From: HediaTnani <hediatnani0@gmail.com>
Date: Fri, 12 Jan 2024 16:47:30 -0500
Subject: [PATCH] Validate qsvPCs is a prcomp object

---
 R/get_qsvs.R                   | 17 +++++++++++------
 tests/testthat/test-get_qsvs.R |  4 ++++
 2 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/R/get_qsvs.R b/R/get_qsvs.R
index d1e767e..42088d5 100644
--- 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
index d785a26..e9f39ab 100644
--- 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.")
 })
\ No newline at end of file