Add loom2sce and sce2loom

Author: nh3

DESCRIPTION

@@ -11,6 +11,7 @@ Depends:
     reticulate
 Imports:
     Seurat (>= 3.0.1),
-    SingleCellExperiment (>= 1.4.0)
+    SingleCellExperiment (>= 1.4.0),
+    LoomExperiment (>= 1.1.5)
 License: GPL-3
 LazyDate: true

R/functions.R

@@ -122,3 +122,11 @@ loom2anndata <- function(
 
     adata
 }
+
+sce2loom <- function(obj, outFile, main_layer = NULL, ...) {
+    writeExchangeableLoom(obj, outFile, main_layer = main_layer, ...)
+}
+
+loom2sce <- function(inFile, outFile = NULL, main_layer = NULL, ...) {
+    readExchangeableLoom(inFile, backed = FALSE, ...)
+}

R/methods.R

@@ -1,11 +1,15 @@
 convertFormat <- function(
-    obj, from = c('seurat', 'sce', 'loom'), to = c('anndata'), outFile = NULL,
+    obj, from = c('seurat', 'sce', 'loom'), to = c('anndata', 'loom', 'sce'), outFile = NULL,
     main_layer = NULL, ...
 ) {
     from <- match.arg(from)
     to <- match.arg(to)
 
-    func <- eval(parse(text=paste(from, to, sep='2')))
+    tryCatch({
+        func <- eval(parse(text = paste(from, to, sep='2')))
+    }, error = function(e) {
+        stop(paste0('Unsupported conversion from "', from, '" to "', to, '"'), call. = FALSE)
+    }, finally = {})
 
     return(func(obj, outFile = outFile, main_layer = main_layer, ...))
 }