Conversion from & to SingleCellExperiment

NAMESPACE

@@ -6,6 +6,7 @@ export(from_SingleCellExperiment)
 export(generate_dataset)
 export(read_h5ad)
 export(to_Seurat)
+export(to_SingleCellExperiment)
 export(write_h5ad)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,sparseMatrix)

R/AbstractAnnData.R

@@ -169,8 +169,37 @@ AbstractAnnData <- R6::R6Class("AbstractAnnData", # nolint
       names(self$uns)
     },
     #' @description Convert to SingleCellExperiment
-    to_SingleCellExperiment = function() {
-      to_SingleCellExperiment(self)
+    #'
+    #' See [to_SingleCellExperiment()] for more details on the conversion.
+    #'
+    #' @param assays_mapping A named list mapping SingleCellExperiment assays to AnnData layers
+    #' @param colData_mapping A named list mapping SingleCellExperiment colData to AnnData obs
+    #' @param rowData_mapping A named list mapping SingleCellExperiment rowData to AnnData var
+    #' @param reduction_mapping A named list mapping SingleCellExperiment reductions to AnnData obsm/varm
+    #' @param colPairs_mapping A named list mapping SingleCellExperiment colPairs to AnnData obsp/varp
+    #' @param rowPairs_mapping A named list mapping SingleCellExperiment rowPairs to AnnData obsp/varp
+    #' @param metadata_mapping A named list mapping SingleCellExperiment metadata to AnnData uns
+    #'
+    #' @return A SingleCellExperiment object
+    to_SingleCellExperiment = function(
+      assays_mapping = NULL,
+      colData_mapping = NULL, # nolint
+      rowData_mapping = NULL, # nolint
+      reduction_mapping = NULL,
+      colPairs_mapping = NULL, # nolint
+      rowPairs_mapping = NULL, # nolint
+      metadata_mapping = NULL
+    ) {
+      to_SingleCellExperiment(
+        self,
+        assays_mapping = assays_mapping,
+        colData_mapping = colData_mapping,
+        rowData_mapping = rowData_mapping,
+        reduction_mapping = reduction_mapping,
+        colPairs_mapping = colPairs_mapping, # nolint
+        rowPairs_mapping = rowPairs_mapping, # nolint
+        metadata_mapping = metadata_mapping
+      )
     },
     #' @description Convert to Seurat
     #'