unit test for predict_gt_pca

EvolEcolGroup · May 8, 2024 · e16cdf9 · e16cdf9
1 parent 427c9c0
commit e16cdf9
Showing 1 changed file with 12 additions and 0 deletions.
diff --git a/tests/testthat/test_gt_pca.R b/tests/testthat/test_gt_pca.R
@@ -0,0 +1,12 @@
+test_that("fit_gt_pca_and_predict",{
+  bed_file <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
+  missing_gt <- gen_tibble(bed_file,  backingfile = tempfile("missing_"),quiet=TRUE)
+  expect_error( missing_gt %>% gt_pca_partialSVD(),
+                "You can't have missing")
+  missing_gt <- gt_impute_simple(missing_gt)
+  missing_pca <- missing_gt %>% gt_pca_partialSVD()
+  expect_true(all.equal(predict(missing_pca),
+                        predict(missing_pca, new_data = missing_gt),
+                        check.attributes=FALSE))
+})
+