@@ -53,7 +53,7 @@ exportSCEtoAnnData <- function(sce,

   AssayName <- SummarizedExperiment::assayNames(sce)

   for (assay in AssayName){

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

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

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

     }

   }

@@ -597,9 +597,9 @@ importCellRanger <- function(

 #' # 2.1.0/pbmc4k

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

 #' sce <- importCellRangerV2(

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

-#'     sampleDirs = "pbmc_800",

-#'     sampleNames = "pbmc4k_800",

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

+#'     sampleDirs = "pbmc_4k_v2_200x400",

+#'     sampleNames = "pbmc4k_400",

 #'     reference = 'GRCh38',

 #'     dataTypeV2 = "filtered")

 #' @export

@@ -662,9 +662,9 @@ importCellRangerV2 <- function(

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

 #' @examples

 #' sce <- importCellRangerV2Sample(

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

+#'     dataDir = system.file("extdata/pbmc_4k_v2_200x400/outs/",

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

-#'     sampleName = "pbmc800")

+#'     sampleName = "pbmc400")

 #' @export

 importCellRangerV2Sample <- function(

     dataDir = NULL,

@@ -277,7 +277,7 @@ distinctColors <- function(n, hues = c("red", "cyan", "orange", "blue",

   for (i in 1:chuN) {

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

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

-    if (is(x, 'DelayedMatrix')) {

+    if (methods::is(x, 'DelayedMatrix')) {

       Mat[[i]] <- methods::as(x[, start:end], "Matrix") # Efficient way to convert DelayedArray to dgCMatrix

     } else {

       Mat[[i]] <- methods::as(x[, start:end], "dgCMatrix") # Convert dgTMatrix to dgCMatrix

@@ -185,7 +185,7 @@ runScrublet <- function(inSCE,

                                               n_neighbors=as.integer(nNeighbors), 

                                               min_dist=minDist)

       }

-      reducedDim(inSCE,'UMAP') <- umap_coordinates

+      reducedDim(inSCE,'scrublet_UMAP') <- umap_coordinates

     if (is.null(tsneAngle) && is.null(tsnePerplexity)){

       tsne_coordinates <- scrublet$get_tsne(scr$manifold_obs_)

@@ -194,7 +194,7 @@ runScrublet <- function(inSCE,

                                             angle=tsneAngle, 

                                             perplexity=as.integer(tsnePerplexity))

     }

-    reducedDim(inSCE,'TSNE') <- tsne_coordinates

+    reducedDim(inSCE,'scrublet_TSNE') <- tsne_coordinates

   }

     colData(inSCE) = cbind(colData(inSCE), output)

@@ -47,7 +47,7 @@ sceOutput <- function(dropletSCE, filteredSCE, samplename, directory){

         ## Export to Python AnnData

         fn <- file.path(directory, samplename, "Python", "Droplets")

-        exportSCEtoAnnData(mergedDropletSCE, outputDir=fn, compression='gzip', sample=samplename)

+        exportSCEtoAnnData(mergedDropletSCE, outputDir=fn, compression='gzip', prefix=samplename)

     }

     if (!is.null(mergedFilteredSCE)) {

@@ -61,7 +61,7 @@ sceOutput <- function(dropletSCE, filteredSCE, samplename, directory){

         ## Export to Python AnnData

         fn <- file.path(directory, samplename, "Python", "FilteredCells")

-        exportSCEtoAnnData(mergedFilteredSCE, outputDir=fn, compression='gzip', sample=samplename)

+        exportSCEtoAnnData(mergedFilteredSCE, outputDir=fn, compression='gzip', prefix=samplename)

   }

 }

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/filtered_gene_bc_matrices/GRCh38/barcodes.tsv

rename to inst/extdata/pbmc_4k_v2_200x400/outs/filtered_gene_bc_matrices/GRCh38/barcodes.tsv

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/filtered_gene_bc_matrices/GRCh38/genes.tsv

rename to inst/extdata/pbmc_4k_v2_200x400/outs/filtered_gene_bc_matrices/GRCh38/genes.tsv

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/filtered_gene_bc_matrices/GRCh38/matrix.mtx

rename to inst/extdata/pbmc_4k_v2_200x400/outs/filtered_gene_bc_matrices/GRCh38/matrix.mtx

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/raw_gene_bc_matrices/GRCh38/barcodes.tsv

rename to inst/extdata/pbmc_4k_v2_200x400/outs/raw_gene_bc_matrices/GRCh38/barcodes.tsv

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/raw_gene_bc_matrices/GRCh38/genes.tsv

rename to inst/extdata/pbmc_4k_v2_200x400/outs/raw_gene_bc_matrices/GRCh38/genes.tsv

similarity index 100%

rename from inst/extdata/pbmc_4k_v2_200x800/pbmc_800/outs/raw_gene_bc_matrices/GRCh38/matrix.mtx

rename to inst/extdata/pbmc_4k_v2_200x400/outs/raw_gene_bc_matrices/GRCh38/matrix.mtx

@@ -202,9 +202,9 @@ sce <- importCellRanger(

 # 2.1.0/pbmc4k

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

 sce <- importCellRangerV2(

-    cellRangerDirs = system.file("extdata/pbmc_4k_v2_200x800", package = "singleCellTK"),

-    sampleDirs = "pbmc_800",

-    sampleNames = "pbmc4k_800",

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

+    sampleDirs = "pbmc_4k_v2_200x400",

+    sampleNames = "pbmc4k_400",

     reference = 'GRCh38',

     dataTypeV2 = "filtered")

 sce <- importCellRangerV3(

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

 }

 \examples{

 sce <- importCellRangerV2Sample(

-    dataDir = system.file("extdata/pbmc_4k_v2_200x800/pbmc_800/outs/",

+    dataDir = system.file("extdata/pbmc_4k_v2_200x400/outs/",

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

-    sampleName = "pbmc800")

+    sampleName = "pbmc400")

 }