@@ -48,9 +48,13 @@ exportSCEtoAnnData <- function(sce,

             " correct Python environment.")

     return(sce)}

-  if (!is(SummarizedExperiment::assay(sce), 'dgCMatrix')) {

-    SummarizedExperiment::assay(sce) <- .convertToMatrix(SummarizedExperiment::assay(sce))

+  AssayName <- SummarizedExperiment::assayNames(sce)

+  for (assay in AssayName){

+    if (!is(SummarizedExperiment::assay(sce, assay), 'dgCMatrix')) {

+      SummarizedExperiment::assay(sce, assay) <- .convertToMatrix(SummarizedExperiment::assay(sce, assay))

+    }

   }

+

   dir.create(outputDir, showWarnings = FALSE, recursive = TRUE)

   annData <- .sce2adata(sce,useAssay)

@@ -597,8 +597,8 @@ importCellRanger <- function(

 #' # 2.1.0/pbmc4k

 #' # All genes are kept. 840 cell barcodes are extracted.

 #' sce <- importCellRangerV2(

-#'     cellRangerDirs = system.file("extdata/", package = "singleCellTK"),

-#'     sampleDirs = "pbmc_4k_v2_200x800",

+#'     cellRangerDirs = system.file("extdata/pbmc_4k_v2_200x800", package = "singleCellTK"),

+#'     sampleDirs = "pbmc_800",

 #'     sampleNames = "pbmc4k_800",

 #'     reference = 'GRCh38',

 #'     dataTypeV2 = "filtered")

@@ -662,7 +662,7 @@ importCellRangerV2 <- function(

 #'  matrix, the feature annotations, and the cell annotation for the sample.

 #' @examples

 #' sce <- importCellRangerV2Sample(

-#'     dataDir = system.file("extdata/pbmc_4k_v2_200x800/outs/",

+#'     dataDir = system.file("extdata/pbmc_4k_v2_200x800/pbmc_800/outs/",

 #'         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),

 #'     sampleName = "pbmc800")

 #' @export

@@ -271,14 +271,15 @@ distinctColors <- function(n, hues = c("red", "cyan", "orange", "blue",

   rn <- rownames(x)

   limit <- (2^32/2-1)

   dimN <- dim(x)

-  chuS <- floor(floor(limit/dimN[1]))

-  chuN <- ceiling(dimN[2]/chuS)

+  chuS <- floor(floor(limit/dimN[1])) # size of chunk

+  chuN <- ceiling(dimN[2]/chuS) # number of chunks

   Mat <- list()

   for (i in 1:chuN) {

     start <- (i-1)*chuS + 1

     end <- min(i*chuS, dimN[2])

-    Mat[[i]] <- methods::as(x[, start:end], "Matrix")

+    Mat[[i]] <- methods::as(x[, start:end], "dgTMatrix")

+    Mat[[i]] <- methods::as(Mat[[i]], "dgCMatrix") #efficient way

   }

   x <- do.call(base::cbind, Mat)

   colnames(x) <- cn

@@ -61,7 +61,6 @@ opt <- arguments$options

 process <- unlist(strsplit(opt$preproc, ','))

 sample <- unlist(strsplit(opt$sample, ','))

 directory <- unlist(strsplit(opt$directory, ','))

-reference <- unlist(strsplit(opt$ref, ','))

 gmt <- opt$gmt

 sep <- opt$delim

 if (!is.null(opt$base_path)) {

@@ -79,7 +78,11 @@ if (!is.null(opt$raw_expr_path)) {

 } else {

     RawDir <- opt$raw_expr_path

 }

-

+if (!is.null(opt$ref)) {

+    reference <- unlist(strsplit(opt$ref, ','))

+} else {

+    reference <- opt$ref

+}

 ## checking argument

 if (is.null(basepath)) {

     if (is.null(FilterDir) || is.null(RawDir)) {

@@ -203,7 +203,7 @@ sce <- importCellRanger(

 # All genes are kept. 840 cell barcodes are extracted.

 sce <- importCellRangerV2(

     cellRangerDirs = system.file("extdata/", package = "singleCellTK"),

-    sampleDirs = "pbmc_4k_v2_800",

+    sampleDirs = "pbmc_4k_v2_200x800",

     sampleNames = "pbmc4k_800",

     reference = 'GRCh38',

     dataTypeV2 = "filtered")

@@ -36,7 +36,7 @@ Read the filtered barcodes, features, and matrices for all

 }

 \examples{

 sce <- importCellRangerV2Sample(

-    dataDir = system.file("extdata/pbmc_4k_v2_800/outs/",

+    dataDir = system.file("extdata/pbmc_4k_v2_200x800/outs/",

         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),

     sampleName = "pbmc800")

 }