Allow loom2sce to save files directly

cellgeni · Sep 25, 2019 · c6ca65a · c6ca65a
1 parent 07c05b0
commit c6ca65a
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Showing 3 changed files with 8 additions and 4 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -3,8 +3,8 @@ Type: Package
 Title: A package to help convert different single-cell data formats to each other
 Version: 0.0.1
 Authors@R: c(
-    person('Vladimir', 'Kiselev', email='wikiselev@users.noreply.github.com', role='cre'),
-    person('Ni', 'Huang', email='nh3@users.noreply.github.com', role='aut'))
+    person('Ni', 'Huang', email='nh3@users.noreply.github.com', role='cre'),
+    person('Vladimir', 'Kiselev', email='wikiselev@users.noreply.github.com', role='aut'))
 Description: Convert Seurat, SingleCellExperiment, Loom object to AnnData object
 Depends:
     R (>= 3.5.1),

diff --git a/R/functions.R b/R/functions.R
@@ -102,7 +102,7 @@ sce2anndata <- function(
     )
 
     if (!is.null(outFile))
-        anndata$AnnData$write(adata, outFile, compression = 'gzip')
+        adata$write(outFile, compression = 'gzip')
 
     adata
 }
@@ -140,5 +140,9 @@ sce2loom <- function(obj, outFile, main_layer = NULL, ...) {
 }
 
 loom2sce <- function(inFile, outFile = NULL, main_layer = NULL, ...) {
-    readExchangeableLoom(inFile, backed = FALSE, ...)
+    sce <- readExchangeableLoom(inFile, backed = FALSE, ...)
+    if (!is.null(outFile))
+        saveRDS(sce, outFile)
+
+    sce
 }
diff --git a/R/loom_utils.R b/R/loom_utils.R