Fixing bug in transform_dataset

Plant-Food-Research-Open · Jan 17, 2024 · f884dfb · f884dfb
1 parent 9669d7d
commit f884dfb
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Showing 2 changed files with 18 additions and 2 deletions.
diff --git a/R/transformation.R b/R/transformation.R
@@ -281,7 +281,13 @@ transform_dataset <- function(mo_data,
                               verbose = TRUE,
                               method,
                               ...) {
-  mo_data <- check_input_multidataset(mo_data, dataset)
+  ## We don't want to subset the dataset
+  check_is_multidataset(mo_data)
+  .check_names(
+    dataset,
+    names(mo_data),
+    "'_W_' datasets are not present in mo_data. Possible dataset names are: '_C_'."
+  )
 
   .check_names(
     transformation,
@@ -569,7 +575,7 @@ transformation_datasets_factory <- function(mo_data_target,
 #' @export
 get_table_transformations <- function(transformation_result, best_normalize_details = FALSE) {
   ## for devtools::check
-  Features <- NULL
+  Features <- Feature <- NULL
 
   transf_name <- c(
     "vsn" = "Variance Stabilising Normalisation (vsn)",

diff --git a/tests/testthat/test-transformation.R b/tests/testthat/test-transformation.R
@@ -141,5 +141,15 @@ test_that("transform_dataset works", {
   )
   expect_error(transform_dataset(multiomics_set, "snps+A", "best-normalize-manual"), "'method' argument should be provided for 'best-normalize-manual' transformation.")
 
+  res <- transform_dataset(
+    multiomics_set,
+    "rnaseq",
+    "best-normalize-manual",
+    method = "center_scale",
+    return_multidataset = TRUE
+  )
+  expect_s4_class(res, "MultiDataSet")
+  expect_equal(names(res), c("snps+A", "rnaseq", "metabolome", "phenotypes"))
+
   # expect_message(transform_dataset(multiomics_set, dataset = "snps+A", transformation = "best-normalize-auto", method = "center_scale"))
 })