Convert MAE to TreeSE and back

R/AllGenerics.R

@@ -410,3 +410,13 @@ setGeneric("addMDS", signature = "x", function(x, ...)
 #' @export
 setGeneric("getReducedDimAttribute", signature = "x", function(x, ...)
     standardGeneric("getReducedDimAttribute"))
+
+#' @rdname utilization_functions
+#' @export
+setGeneric("convertToMAE", signature = "x", function(x, ...)
+    standardGeneric("convertToMAE"))
+
+#' @rdname utilization_functions
+#' @export
+setGeneric("convertToTreeSE", signature = "x", function(x, ...)
+    standardGeneric("convertToTreeSE"))

R/utilization_functions.R

@@ -49,7 +49,6 @@
 #'
 NULL
 
-#'
 #' @export
 #' @rdname utilization_functions
 #' @importFrom SingleCellExperiment reducedDim
@@ -69,6 +68,35 @@ setMethod("getReducedDimAttribute", "SingleCellExperiment",
     }
 )
 
+#' @export
+#' @rdname utilization_functions
+#' @importFrom SingleCellExperiment reducedDims
+setMethod("convertToMAE", "SingleCellExperiment",
+    function(x, name = "main", ...){
+        exps <- setNames(list(x), name)
+        exps <- c(exps, altExps(x) |> as.list()) |> ExperimentList()
+        mae <- MultiAssayExperiment(experiments = exps, colData = colData(x))
+        return(mae)
+    }
+)
+
+#' @export
+#' @rdname utilization_functions
+#' @importFrom MultiAssayExperiment intersectColumns experiments
+setMethod("convertToTreeSE", "MultiAssayExperiment",
+    function(x, ...){
+        x <- intersectColumns(x)
+        exps <- experiments(x)
+        if( !all(vapply(exps, function(x) is(x, "SummarizedExperiment"), logical(1L))) ){
+            stop("All experiments must be SummarizedExperiment objects.", call. = FALSE)
+        }
+        tse <- exps[[1L]] |> as("TreeSummarizedExperiment")
+        altExps(tse) <- exps[-1]
+        return(tse)
+    }
+)
+
+
 ################################ HELP FUNCTIONS ################################
 
 # From a list, extract those elements that user has specified