Merge pull request #25 from stemangiola/seurat

Seurat output

Author: stemangiola

DESCRIPTION

@@ -23,19 +23,20 @@ Imports:
 	RSQLite,
 	dbplyr
 Suggests:
-	here,
-	stringr,
-	Seurat,
-	tidyseurat,
-	scMerge,
-	DelayedArray,
-	openssl,
-	cellxgenedp,
-	SingleCellExperiment,
-	celldex,
-	SingleR,
-	tools,
-	rmarkdown
+    here,
+    stringr,
+    Seurat,
+    tidyseurat,
+    scMerge,
+    DelayedArray,
+    openssl,
+    cellxgenedp,
+    SingleCellExperiment,
+    celldex,
+    SingleR,
+    tools,
+    rmarkdown,
+    SeuratObject
 VignetteBuilder:
     knitr
 RdMacros:

NAMESPACE

@@ -1,13 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as.sparse,DelayedMatrix)
 export(get_SingleCellExperiment)
 export(get_metadata)
+export(get_seurat)
 importFrom(BiocGenerics,cbind)
 importFrom(DBI,dbConnect)
 importFrom(HDF5Array,HDF5RealizationSink)
 importFrom(HDF5Array,loadHDF5SummarizedExperiment)
 importFrom(RSQLite,SQLITE_RO)
 importFrom(RSQLite,SQLite)
+importFrom(Seurat,as.Seurat)
+importFrom(SeuratObject,as.sparse)
 importFrom(SingleCellExperiment,SingleCellExperiment)
 importFrom(SummarizedExperiment,"assayNames<-")
 importFrom(SummarizedExperiment,colData)

R/query.R

@@ -78,6 +78,25 @@ get_SingleCellExperiment = function(
 	sce
 }
 
+#' @importFrom SeuratObject as.sparse
+#' @exportS3Method 
+as.sparse.DelayedMatrix = function(x){
+  # This is glue to ensure the SCE -> Seurat conversion works properly with
+  # DelayedArray types
+  as(x, "dgCMatrix")
+}
+
+#' Given a data frame of HCA metadata, returns a Seurat object corresponding to the samples in that data frame
+#'
+#' @inheritDotParams get_SingleCellExperiment
+#' @importFrom Seurat as.Seurat 
+#' @export
+get_seurat = function(
+  ...
+){
+  get_SingleCellExperiment(...) |> as.Seurat(data=NULL)
+}
+
 
 #' Returns a data frame of Human Cell Atlas metadata, which should be filtered
 #' and ultimately passed into get_SingleCellExperiment.

man/get_seurat.Rd

@@ -13,3 +13,18 @@ test_that("The genes argument to get_SingleCellExperiment subsets genes", {
 
   expect_gt(sce_full, sce_subset)
 })
+
+test_that("get_seurat() returns the appropriate data in Seurat format", {
+  meta = get_metadata() |> head(2)
+  
+  sce = get_SingleCellExperiment(meta, genes = "PUM1")
+  seurat = get_seurat(meta, genes = "PUM1")
+  
+  # The output should be a Seurat object
+  expect_s4_class(seurat, "Seurat")
+  # Both methods should have appropriately subset genes
+  expect_equal(
+    rownames(sce),
+    rownames(seurat)
+  )
+})