Warn about gene id conversions,

AlexsLemonade · Dec 9, 2024 · 36296d9 · 36296d9
1 parent 9ef3821
commit 36296d9
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Showing 4 changed files with 11 additions and 4 deletions.
diff --git a/R/convert-gene-ids.R b/R/convert-gene-ids.R
@@ -94,6 +94,9 @@ ensembl_to_symbol <- function(
   }
 
   if (seurat_compatible) {
+    if (any(grepl("_", gene_symbols))) {
+      warning("Replacing underscores ('_') with dashes ('-') in gene symbols for Seurat compatibility.")
+    }
     gene_symbols <- gsub("_", "-", gene_symbols)
   }
 

diff --git a/R/make-seurat.R b/R/make-seurat.R
@@ -100,10 +100,10 @@ sce_to_seurat <- function(
   # convert and set functions depending on assay version requested
   if (seurat_assay_version == "v5") {
     create_seurat_assay <- SeuratObject::CreateAssay5Object
-    sobj[["RNA"]] <- as(sobj[["RNA"]], "Assay5")
+    suppressWarnings(sobj[["RNA"]] <- as(sobj[["RNA"]], "Assay5"))
   } else {
     create_seurat_assay <- SeuratObject::CreateAssayObject
-    sobj[["RNA"]] <- as(sobj[["RNA"]], "Assay")
+    suppressWarnings(sobj[["RNA"]] <- as(sobj[["RNA"]], "Assay"))
   }
 
   # add spliced data if present

diff --git a/tests/testthat/test-convert-gene-ids.R b/tests/testthat/test-convert-gene-ids.R
@@ -58,7 +58,9 @@ test_that("gene symbol conversion in seurat compatibility mode works", {
   expect_equal(gene_symbols, c("TP53", "MYCN"))
 
   ensembl_ids <- c("ENSG00000285609", "ENSG00000252254", "ENSG00000283274")
-  gene_symbols <- ensembl_to_symbol(ensembl_ids, unique = FALSE, seurat_compatible = TRUE)
+  expect_warning( # this includes name changes for compatibility, so a warning is expected
+    gene_symbols <- ensembl_to_symbol(ensembl_ids, unique = FALSE, seurat_compatible = TRUE)
+  )
   expect_equal(gene_symbols, c("5S-rRNA", "Y-RNA", "5-8S-rRNA"))
 })
 

diff --git a/tests/testthat/test-make-seurat.R b/tests/testthat/test-make-seurat.R
@@ -37,7 +37,9 @@ test_that("SCE to Seurat with no id conversion works", {
 
 test_that("SCE to Seurat with id conversion works as expected", {
   sce <- readRDS(test_path("data", "scpca_sce.rds"))
-  seurat_obj <- sce_to_seurat(sce, use_symbols = TRUE, reference = "sce")
+  expect_warning(
+    seurat_obj <- sce_to_seurat(sce, use_symbols = TRUE, reference = "sce")
+  )
 
   new_genes <- suppressMessages(
     ensembl_to_symbol(rownames(sce), unique = TRUE, sce = sce)