Fix for Seurat updates

welch-lab · Dec 7, 2023 · be62a6d · be62a6d
1 parent cb45fcb
commit be62a6d
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/R/normalize.R b/R/normalize.R
@@ -61,7 +61,7 @@ colNormalize.Seurat <- function(
     value <- .getSeuratData(x, assay = assay, layer = layer, clusterVar = NULL)
     mat <- value[[1]]
     norm <- colNormalize.default(mat, scaleFactor = scaleFactor, log = log)
-    x <- Seurat::SetAssayData(x, slot = "data", assay = assay, new.data = norm)
+    SeuratObject::LayerData(x, layer = "data", assay = assay) <- norm
     return(x)
 }
 

diff --git a/tests/testthat/test-objectS3.R b/tests/testthat/test-objectS3.R
@@ -28,7 +28,8 @@ if (requireNamespace("Seurat", quietly = TRUE) &&
 
     test_that("normalization", {
         srt <- colNormalize(srt)
-        expect_equal(sum(colSums(srt@assays$RNA@data)), ncol(rnaRaw))
+        expect_equal(sum(colSums(LayerData(srt, layer = "data", assay = "RNA"))),
+                     ncol(rnaRaw))
 
         sce <- colNormalize(sce)
         expect_true("normcounts" %in% assayNames(sce))