@@ -69,6 +69,7 @@ setMethod("import", "TENxMTX", function(con, format, text, ...) {

     ## coerce to common use class

     mtxf <- as(mtxf, "CsparseMatrix")

     SummarizedExperiment(

-        assays = S4Vectors::SimpleList(counts = mtxf)

+        assays = S4Vectors::SimpleList(counts = mtxf),

+        metadata = metadata(con)

     )

 })

@@ -14,11 +14,7 @@

 #' @return A `TENxMTX` class object

 #'

 #' @exportClass TENxMTX

-.TENxMTX <- setClass(

-    Class = "TENxMTX",

-    contains = "TENxFile",

-    slots = c(compressed = "logical")

-)

+.TENxMTX <- setClass(Class = "TENxMTX", contains = "TENxFile")

 #' TENxMTX: Represent Matrix Market Format Files from 10X

 #'

@@ -8,8 +8,8 @@

 #'

 #' @details The `TENxMTX` class is a straightforward implementation that allows

 #'   the user to import a Matrix Market file format using `Matrix::readMM`.

-#'   Currently, it only supports return types of `dgCMatrix`. To request other

-#'   formats, please open an issue on GitHub.

+#'   Currently, it returns a `SummarizedExperiment` with an internal `dgCMatrix`

+#'   assay. To request other formats, please open an issue on GitHub.

 #'

 #' @return A `TENxMTX` class object

 #'

@@ -25,17 +25,17 @@

 #' This constructor function accepts `.mtx` and `.mtx.gz` compressed formats

 #' for eventual importing. It is mainly used with tarball files from 10X

 #' Genomics, where more annotation data is included. Importing solely the

-#' `.mtx` format will provide users with a sparse matrix of `dgCMatrix` class

-#' from the `Matrix` package. Currently, other formats are not supported but

-#' if you'd like to request support for a format, please open an issue on

-#' GitHub.

+#' `.mtx` format will provide users with a `SummarizedExperiment` with an assay

+#' of class `dgCMatrix` from the `Matrix` package. Currently, other formats are

+#' not supported but if you'd like to request support for a format, please open

+#' an issue on GitHub.

 #'

 #' @inheritParams TENxFile

 #'

 #' @param compressed logical(1) Whether the resource file is compressed (default

 #'   FALSE)

 #'

-#' @return A `SummarizedExperiment` instance

+#' @return A `SummarizedExperiment` instance with a `dgCMatrix` in the assay

 #'

 #' @examples

 #'

@@ -71,7 +71,7 @@ TENxMTX <- function(resource, compressed = FALSE, ...) {

 setMethod("import", "TENxMTX", function(con, format, text, ...) {

     mtxf <- Matrix::readMM(path(con))

     ## coerce to common use class

-    mtxf <- as(mtxf, "dgCMatrix")

+    mtxf <- as(mtxf, "CsparseMatrix")

     SummarizedExperiment(

         assays = S4Vectors::SimpleList(counts = mtxf)

     )

@@ -11,6 +11,8 @@

 #'   Currently, it only supports return types of `dgCMatrix`. To request other

 #'   formats, please open an issue on GitHub.

 #'

+#' @return A `TENxMTX` class object

+#'

 #' @exportClass TENxMTX

 .TENxMTX <- setClass(

     Class = "TENxMTX",

@@ -33,7 +35,7 @@

 #' @param compressed logical(1) Whether the resource file is compressed (default

 #'   FALSE)

 #'

-#' @return An instance of the `TENxMTX` class

+#' @return A `SummarizedExperiment` instance

 #'

 #' @examples

 #'

@@ -61,6 +61,7 @@ TENxMTX <- function(resource, compressed = FALSE, ...) {

 #' @describeIn TENxMTX Import method mainly for mtx.gz files from 10x

 #'

 #' @importFrom S4Vectors SimpleList

+#' @importFrom Matrix readMM

 #'

 #' @inheritParams BiocIO::import

 #'

@@ -37,8 +37,13 @@

 #'

 #' @examples

 #'

-#' mtxf <-"~/data/10x/pbmc_3k/filtered_feature_bc_matrix/matrix.mtx.gz"

+#' mtxf <- system.file(

+#'     "extdata", "pbmc_3k_ff_bc_ex.mtx",

+#'     package = "TENxIO", mustWork = TRUE

+#' )

+#'

 #' con <- TENxMTX(mtxf)

+#'

 #' import(con)

 #'

 #' @export

@@ -53,7 +53,12 @@ TENxMTX <- function(resource, compressed = FALSE, ...) {

     .TENxMTX(resource = resource, compressed = compr, extension = ext)

 }

+#' @describeIn TENxMTX Import method mainly for mtx.gz files from 10x

+#'

 #' @importFrom S4Vectors SimpleList

+#'

+#' @inheritParams BiocIO::import

+#'

 #' @export

 setMethod("import", "TENxMTX", function(con, format, text, ...) {

     mtxf <- Matrix::readMM(path(con))

@@ -59,7 +59,7 @@ setMethod("import", "TENxMTX", function(con, format, text, ...) {

     mtxf <- Matrix::readMM(path(con))

     ## coerce to common use class

     mtxf <- as(mtxf, "dgCMatrix")

-    SummarizedExperiment::SummarizedExperiment(

-        assays = SimpleList(counts = mtxf)

+    SummarizedExperiment(

+        assays = S4Vectors::SimpleList(counts = mtxf)

     )

 })

@@ -53,6 +53,7 @@ TENxMTX <- function(resource, compressed = FALSE, ...) {

     .TENxMTX(resource = resource, compressed = compr, extension = ext)

 }

+#' @importFrom S4Vectors SimpleList

 #' @export

 setMethod("import", "TENxMTX", function(con, format, text, ...) {

     mtxf <- Matrix::readMM(path(con))

@@ -53,7 +53,6 @@ TENxMTX <- function(resource, compressed = FALSE, ...) {

     .TENxMTX(resource = resource, compressed = compr, extension = ext)

 }

-#' @import SummarizedExperiment

 #' @export

 setMethod("import", "TENxMTX", function(con, format, text, ...) {

     mtxf <- Matrix::readMM(path(con))

@@ -1,12 +1,40 @@

 #' TENxMTX: The Matrix Market representation class for 10X Data

 #'

+#' @description This class is designed to work with 10x MTX datasets,

+#'   particularly from the multiome pipelines.

 #'

+#' @slot compressed logical(1) Whether or not the file is in compressed format,

+#'   usually gzipped (`.gz`).

+#'

+#' @details The `TENxMTX` class is a straightforward implementation that allows

+#'   the user to import a Matrix Market file format using `Matrix::readMM`.

+#'   Currently, it only supports return types of `dgCMatrix`. To request other

+#'   formats, please open an issue on GitHub.

+#'

+#' @exportClass TENxMTX

 .TENxMTX <- setClass(

     Class = "TENxMTX",

     contains = "TENxFile",

     slots = c(compressed = "logical")

 )

+#' TENxMTX: Represent Matrix Market Format Files from 10X

+#'

+#' This constructor function accepts `.mtx` and `.mtx.gz` compressed formats

+#' for eventual importing. It is mainly used with tarball files from 10X

+#' Genomics, where more annotation data is included. Importing solely the

+#' `.mtx` format will provide users with a sparse matrix of `dgCMatrix` class

+#' from the `Matrix` package. Currently, other formats are not supported but

+#' if you'd like to request support for a format, please open an issue on

+#' GitHub.

+#'

+#' @inheritParams TENxFile

+#'

+#' @param compressed logical(1) Whether the resource file is compressed (default

+#'   FALSE)

+#'

+#' @return An instance of the `TENxMTX` class

+#'

 #' @examples

 #'

 #' mtxf <-"~/data/10x/pbmc_3k/filtered_feature_bc_matrix/matrix.mtx.gz"

@@ -1,13 +1,36 @@

+#' TENxMTX: The Matrix Market representation class for 10X Data

+#'

+#'

 .TENxMTX <- setClass(

     Class = "TENxMTX",

-    contains = "TENxFile"

+    contains = "TENxFile",

+    slots = c(compressed = "logical")

 )

+#' @examples

+#'

+#' mtxf <-"~/data/10x/pbmc_3k/filtered_feature_bc_matrix/matrix.mtx.gz"

+#' con <- TENxMTX(mtxf)

+#' import(con)

+#'

+#' @export

+TENxMTX <- function(resource, compressed = FALSE, ...) {

+    dots <- list(...)

+    ext <- dots[["extension"]]

+    if (is.null(ext))

+        ext <- .get_ext(resource)

+    compr <- identical(ext, "mtx.gz")

+    if (!ext %in% c("mtx.gz", "mtx"))

+        warning("File extension is not 'mtx'; import may fail", call. = FALSE)

+    .TENxMTX(resource = resource, compressed = compr, extension = ext)

+}

+

 #' @import SummarizedExperiment

 #' @export

 setMethod("import", "TENxMTX", function(con, format, text, ...) {

-    mtxf <- SingleCellMultiModal:::.read_mtx(path(con))

-    ## TODO: make use of other files

+    mtxf <- Matrix::readMM(path(con))

+    ## coerce to common use class

+    mtxf <- as(mtxf, "dgCMatrix")

     SummarizedExperiment::SummarizedExperiment(

         assays = SimpleList(counts = mtxf)

     )

new file mode 100644

@@ -0,0 +1,14 @@

+.TENxMTX <- setClass(

+    Class = "TENxMTX",

+    contains = "TENxFile"

+)

+

+#' @import SummarizedExperiment

+#' @export

+setMethod("import", "TENxMTX", function(con, format, text, ...) {

+    mtxf <- SingleCellMultiModal:::.read_mtx(path(con))

+    ## TODO: make use of other files

+    SummarizedExperiment::SummarizedExperiment(

+        assays = SimpleList(counts = mtxf)

+    )

+})