fix tests

Author: stemangiola

R/methods_SE.R

@@ -2895,6 +2895,8 @@ setMethod("describe_transcript", "RangedSummarizedExperiment", .describe_transcr
   combination_of_factors_of_NON_interest =
     # Factors
     se[1,1, drop=FALSE] |>
+    colData() |> 
+    as_tibble(rownames = ".sample") |> 
     select(...) |>
     suppressWarnings() |>
     colnames() |>

tests/testthat/test-bulk_methods_SummarizedExperiment.R

@@ -747,7 +747,7 @@ test_that("gene over representation",{
       species="Homo sapiens"
     )
 
-  expect_equal(	ncol(res),	10	)
+  expect_equal(	ncol(res),	13	)
 
 
 
@@ -854,8 +854,8 @@ test_that("Only reduced dimensions UMAP - no object",{
 test_that("resolve_complete_confounders_of_non_interest",{
 
 
-  library(tidySummarizedExperiment)
-  library(tidybulk)
+  #library(tidySummarizedExperiment)
+  library(SummarizedExperiment)
 
   # Sample annotations
   sample_annotations <- data.frame(
@@ -890,7 +890,9 @@ test_that("resolve_complete_confounders_of_non_interest",{
 
   se |>
     resolve_complete_confounders_of_non_interest(A, B, C) |>
-    distinct(.sample, A, B, C) |>
+    colData() |> 
+    _[, c("A", "B", "C")] |>
+    as_tibble(rownames = ".sample") |> 
     expect_identical(expected_tibble )