Update utils.R

#40 compatible with Seurat 5
ZJUFanLab · Jun 14, 2024 · 8ee1042 · 8ee1042
1 parent df5b507
commit 8ee1042
Showing 1 changed file with 11 additions and 1 deletion.
diff --git a/R/utils.R b/R/utils.R
@@ -286,7 +286,17 @@
 .normalize_data <- function(rawdata) {
  rawdata <- Seurat::CreateSeuratObject(rawdata)
  rawdata <- Seurat::NormalizeData(rawdata, verbose = F)
- rawdata <- rawdata[["RNA"]]@data
+ ver <- packageVersion("Seurat")
+ ver <- substr(ver,1,1)
+ if (ver >= 5) {
+ genenames <- rownames(rawdata)
+ cellnames <- colnames(rawdata)
+ rawdata <- rawdata[["RNA"]]@layers$data
+ rownames(rawdata) <- genenames
+ colnames(rawdata) <- cellnames
+ } else {
+ rawdata <- rawdata[["RNA"]]@data
+ }
  return(rawdata)
 }