Merge pull request #84 from myushen/master

rename assay names for consistency
MangiolaLaboratory · Nov 14, 2024 · 476f692 · 476f692
2 parents dfb080d + f61b7aa
commit 476f692
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Showing 2 changed files with 5 additions and 1 deletion.
diff --git a/NAMESPACE b/NAMESPACE
@@ -131,6 +131,7 @@ importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SingleCellExperiment,altExp)
 importFrom(SingleR,SingleR)
 importFrom(SummarizedExperiment,"assay<-")
+importFrom(SummarizedExperiment,"assays<-")
 importFrom(SummarizedExperiment,"colData<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,SummarizedExperiment)

diff --git a/R/tranform_assay.R b/R/tranform_assay.R
@@ -58,7 +58,7 @@ transform_assay.HPCell = function(
 #'
 #' @importFrom SummarizedExperiment assay
 #' @importFrom SummarizedExperiment assay<-
-#' @importFrom SummarizedExperiment assays
+#' @importFrom SummarizedExperiment assays assays<-
 #' @importFrom SummarizedExperiment rowData
 #' @importFrom SummarizedExperiment rowData<-
 #' @importFrom SingleCellExperiment reducedDim<-
@@ -75,6 +75,9 @@ transform_utility  = function(input_read_RNA_assay, transform_fx, external_path,
 
   if(ncol(input_read_RNA_assay) == 0) return(NULL)
 
+  # Rename assay names to for consistency
+  if (names(assays(input_read_RNA_assay)) != "X") names(assays(input_read_RNA_assay)) <- "X"
+
   # strip metadata that we don't need
   input_read_RNA_assay = 
     input_read_RNA_assay |>