116: sanitize error message from vst (#117)

Author: danielinteractive

R/normalization.R

@@ -230,10 +230,18 @@ h_vst <- function(object,
     is_hermes_data(object),
     is_list_with(control, "fit_type")
   )
-  DESeq2::varianceStabilizingTransformation(
-    counts(object),
-    fitType = control$fit_type
-  )
+  tryCatch({
+    DESeq2::varianceStabilizingTransformation(
+      counts(object),
+      fitType = control$fit_type
+    )
+  },
+  error = function(e) {
+    stop(paste(
+      "During calculation of variance-stabilized transformation (VST) hit error,",
+      "try again with more genes. Original error:", e
+    ))
+  })
 }
 
 #' @describeIn normalize regularized log transformation (`rlog`) from `DESeq2` package.

tests/testthat/test-normalization.R

@@ -236,6 +236,14 @@ test_that("h_vst fails when there are no genes", {
   expect_error(h_vst(object))
 })
 
+test_that("h_vst gives understandable error for an object with few genes", {
+  object <- HermesData(get_se())
+  expect_error(
+    h_vst(object),
+    "try again with more genes"
+  )
+})
+
 # h_rlog ----
 
 test_that("h_rlog function works as expected with default settings", {