@@ -46,9 +46,16 @@ fl <- system.file(

 ## Method 1 (tarball)

 TENxFileList(fl)

+## metadata before import

+metadata(TENxFileList(fl))

+

 ## import() method

 import(TENxFileList(fl))

+## metadata after import

+import(TENxFileList(fl)) |>

+    metadata()

+

 ## untar to simulate folder output

 dir.create(tdir <- tempfile())

 untar(fl, exdir = tdir)

@@ -7,8 +7,8 @@

 TENxFileList(..., version, compressed = FALSE)

 }

 \arguments{

-\item{...}{A single file path, named arguments corresponding to file paths,

-or a list of named file paths}

+\item{...}{Typically, a file path to a tarball archive. Can be named

+arguments corresponding to file paths, or a named list of file paths.}

 \item{version}{character(1) The version in the tarball. See details.}

@@ -43,6 +43,37 @@ fl <- system.file(

     package = "TENxIO", mustWork = TRUE

 )

+## Method 1 (tarball)

+TENxFileList(fl)

+

+## import() method

 import(TENxFileList(fl))

+## untar to simulate folder output

+dir.create(tdir <- tempfile())

+untar(fl, exdir = tdir)

+

+## Method 2 (folder)

+TENxFileList(tdir)

+import(TENxFileList(tdir))

+

+## Method 3 (list of TENxFile objects)

+files <- list.files(tdir, recursive = TRUE, full.names = TRUE)

+names(files) <- basename(files)

+filelist <- lapply(files, TENxFile)

+

+TENxFileList(filelist, compressed = FALSE)

+

+## Method 4 (SimpleList)

+TENxFileList(as(filelist, "SimpleList"), compressed = FALSE)

+

+## Method 5 (named arguments)

+TENxFileList(

+    barcodes.tsv.gz = TENxFile(files[1]),

+    features.tsv.gz = TENxFile(files[2]),

+    matrix.mtx.gz = TENxFile(files[3])

+)

+

+unlink(tdir, recursive = TRUE)

+

 }

@@ -7,8 +7,8 @@

 TENxFileList(..., version, compressed = FALSE)

 }

 \arguments{

-\item{...}{Typically, a file path to a tarball archive. Can be named

-arguments corresponding to file paths, or a named list of file paths.}

+\item{...}{A single file path, named arguments corresponding to file paths,

+or a list of named file paths}

 \item{version}{character(1) The version in the tarball. See details.}

@@ -43,37 +43,6 @@ fl <- system.file(

     package = "TENxIO", mustWork = TRUE

 )

-## Method 1 (tarball)

-TENxFileList(fl)

-

-## import() method

 import(TENxFileList(fl))

-## untar to simulate folder output

-dir.create(tdir <- tempfile())

-untar(fl, exdir = tdir)

-

-## Method 2 (folder)

-TENxFileList(tdir)

-import(TENxFileList(tdir))

-

-## Method 3 (list of TENxFile objects)

-files <- list.files(tdir, recursive = TRUE, full.names = TRUE)

-names(files) <- basename(files)

-filelist <- lapply(files, TENxFile)

-

-TENxFileList(filelist, compressed = FALSE)

-

-## Method 4 (SimpleList)

-TENxFileList(as(filelist, "SimpleList"), compressed = FALSE)

-

-## Method 5 (named arguments)

-TENxFileList(

-    barcodes.tsv.gz = TENxFile(files[1]),

-    features.tsv.gz = TENxFile(files[2]),

-    matrix.mtx.gz = TENxFile(files[3])

-)

-

-unlink(tdir, recursive = TRUE)

-

 }

@@ -7,8 +7,8 @@

 TENxFileList(..., version, compressed = FALSE)

 }

 \arguments{

-\item{...}{A single file path, named arguments corresponding to file paths,

-or a list of named file paths}

+\item{...}{Typically, a file path to a tarball archive. Can be named

+arguments corresponding to file paths, or a named list of file paths.}

 \item{version}{character(1) The version in the tarball. See details.}

@@ -43,6 +43,37 @@ fl <- system.file(

     package = "TENxIO", mustWork = TRUE

 )

+## Method 1 (tarball)

+TENxFileList(fl)

+

+## import() method

 import(TENxFileList(fl))

+## untar to simulate folder output

+dir.create(tdir <- tempfile())

+untar(fl, exdir = tdir)

+

+## Method 2 (folder)

+TENxFileList(tdir)

+import(TENxFileList(tdir))

+

+## Method 3 (list of TENxFile objects)

+files <- list.files(tdir, recursive = TRUE, full.names = TRUE)

+names(files) <- basename(files)

+filelist <- lapply(files, TENxFile)

+

+TENxFileList(filelist, compressed = FALSE)

+

+## Method 4 (SimpleList)

+TENxFileList(as(filelist, "SimpleList"), compressed = FALSE)

+

+## Method 5 (named arguments)

+TENxFileList(

+    barcodes.tsv.gz = TENxFile(files[1]),

+    features.tsv.gz = TENxFile(files[2]),

+    matrix.mtx.gz = TENxFile(files[3])

+)

+

+unlink(tdir, recursive = TRUE)

+

 }

@@ -32,8 +32,8 @@ identifiers

 If all above files are in the tarball, the import method will provide a

 \code{SingleCellExperiment}. Otherwise, a simple list of imported data is given.

 Note that version "3" uses 'features.tsv.gz' and version "2" uses

-'genes.tsv.gz'. If known, indicate the version argument in the \code{TENxFileList}

-constructor function.

+'genes.tsv.gz'. If known, indicate the \code{version} argument in the

+\code{TENxFileList} constructor function.

 }

 }

 \examples{

@@ -4,12 +4,14 @@

 \alias{TENxFileList}

 \title{TENxFileList: Represent groups of files from 10X Genomic}

 \usage{

-TENxFileList(..., compressed = FALSE)

+TENxFileList(..., version, compressed = FALSE)

 }

 \arguments{

 \item{...}{A single file path, named arguments corresponding to file paths,

 or a list of named file paths}

+\item{version}{character(1) The version in the tarball. See details.}

+

 \item{compressed}{logical(1) Whether or not the file provided is compressed,

 usually as \code{tar.gz} (default FALSE)}

 }

@@ -29,6 +31,9 @@ These tarballs usually contain three files:

 identifiers

 If all above files are in the tarball, the import method will provide a

 \code{SingleCellExperiment}. Otherwise, a simple list of imported data is given.

+Note that version "3" uses 'features.tsv.gz' and version "2" uses

+'genes.tsv.gz'. If known, indicate the version argument in the \code{TENxFileList}

+constructor function.

 }

 }

 \examples{

@@ -33,7 +33,11 @@ If all above files are in the tarball, the import method will provide a

 }

 \examples{

-fl <- "~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.tar.gz"

-con <- TENxFileList(fl)

+fl <- system.file(

+    "extdata", "pbmc_granulocyte_sorted_3k_ff_bc_ex_matrix.tar.gz",

+    package = "TENxIO", mustWork = TRUE

+)

+

+import(TENxFileList(fl))

 }

new file mode 100644

@@ -0,0 +1,39 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/TENxFileList-class.R

+\name{TENxFileList}

+\alias{TENxFileList}

+\title{TENxFileList: Represent groups of files from 10X Genomic}

+\usage{

+TENxFileList(..., compressed = FALSE)

+}

+\arguments{

+\item{...}{A single file path, named arguments corresponding to file paths,

+or a list of named file paths}

+

+\item{compressed}{logical(1) Whether or not the file provided is compressed,

+usually as \code{tar.gz} (default FALSE)}

+}

+\value{

+Either a \code{SingleCellExperiment} or a list of imported data

+}

+\description{

+This constructor function is meant to handle \code{.tar.gz} tarball

+files from 10X Genomics.

+}

+\details{

+These tarballs usually contain three files:

+\enumerate{

+\item \code{matrix.mtx.gz} - the counts matrix

+\item \code{features.tsv.gz} - row metadata usually represented as \code{rowData}

+\item \code{barcodes.tsv.gz} - column names corresponding to cell barcode

+identifiers

+If all above files are in the tarball, the import method will provide a

+\code{SingleCellExperiment}. Otherwise, a simple list of imported data is given.

+}

+}

+\examples{

+

+fl <- "~/data/10x/pbmc_3k/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.tar.gz"

+con <- TENxFileList(fl)

+

+}