@@ -46,7 +46,7 @@

     }

     mat <- Matrix::readMM(path)

-    mat <- methods::as(mat, "dgCMatrix")

+    mat <- methods::as(mat, "CsparseMatrix")

     if (class == "matrix") {

         mat <- as.matrix(mat)

@@ -124,7 +124,6 @@ importFromFiles <- function(assayFile, annotFile = NULL, featureFile = NULL,

   if (is.null(colnames(countsin))){

     colnames(countsin) <- rownames(annotin)

   }

-  #assaylist[[assayName]] <- methods::as(countsin, "dgCMatrix")

   assaylist[[assayName]] <- .convertToMatrix(countsin)

   newassay <- SingleCellExperiment::SingleCellExperiment(assays = assaylist,

@@ -42,7 +42,7 @@

     ## Convert to "dgCMatrix"

     newM <- Matrix::Matrix(mat[,1], nrow=nrow(mat))

-    newM <- methods::as(newM, "dgCMatrix")

+    newM <- methods::as(newM, "CsparseMatrix")

     breaks <- seq(2, ncol(mat), by=1000)

     if(length(breaks) > 2) {

       for(i in seq(2, length(breaks))) {

@@ -25,7 +25,7 @@

     missMat <- Matrix::Matrix(0, nrow = length(missGene), ncol = ncol(matrix),

         dimnames = list(missGene, NULL))

-    matb <- methods::as(matrix, "dgCMatrix")

+    matb <- methods::as(matrix, "CsparseMatrix")

     rownames(matb) <- rownames(matrix)

     mat <- rbind(matb, missMat)

@@ -177,7 +177,7 @@ discreteColorPalette <- function(n, palette = c("random", "ggplot", "celda"),

   for (i in seq_len(chuN)) {

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

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

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

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

   }

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

   colnames(x) <- cn

@@ -82,7 +82,7 @@

 #' sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 #' \dontrun{

 #' # SoupX does not work for toy example,

-#' # can be tested with `sce <- importExampleData("pbmc3k")`

+#' sce <- importExampleData("pbmc3k")

 #' sce <- runSoupX(sce, sample = "sample")

 #' }

 runSoupX <- function(inSCE,

@@ -1344,7 +1344,7 @@ convertSCEToSeurat <-

     if (!is.null(normAssay) && normAssay %in% names(assays(inSCE))) {

       tempMatrix <- .convertToMatrix(assay(inSCE, normAssay))

       if (inherits(tempMatrix, "dgeMatrix")) {

-        tempMatrix <- methods::as(tempMatrix, "dgCMatrix")

+        tempMatrix <- methods::as(tempMatrix, "CsparseMatrix")

       }

       seuratObject@assays$RNA@data <- tempMatrix

       rownames(seuratObject@assays$RNA@data) <- seuratRowNames

@@ -135,7 +135,7 @@ data(scExample, package = "singleCellTK")

 sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")

 \dontrun{

 # SoupX does not work for toy example,

-# can be tested with `sce <- importExampleData("pbmc3k")`

+sce <- importExampleData("pbmc3k")

 sce <- runSoupX(sce, sample = "sample")

 }

 }