@@ -32,13 +32,14 @@

 \item{con}{The connection from which data is loaded or to which data is

 saved. If this is a \code{character} vector, it is assumed to be a file name and

 a corresponding file connection is created and then closed after exporting

-the object. If it is a \linkS4class{BiocFile} derivative, the data is loaded from

-or saved to the underlying resource. If missing, the function will return

-the output as a character vector, rather than writing to a connection.}

+the object. If it is a \link[BiocIO:BiocFile-class]{BiocFile} derivative, the

+data is loaded from or saved to the underlying resource. If missing, the

+function will return the output as a character vector, rather than writing

+to a connection.}

 \item{format}{The format of the output. If missing and \code{con} is a

 file name, the format is derived from the file extension. This argument is

-unnecessary when \code{con} is a derivative of \linkS4class{BiocFile}.}

+unnecessary when \code{con} is a derivative of \link[BiocIO:BiocFile-class]{BiocFile}.}

 \item{text}{If \code{con} is missing, this can be a character vector directly

 providing the string data to import.}

@@ -7,6 +7,7 @@

 \alias{path,TENxFileList-method}

 \alias{decompress,TENxFileList-method}

 \alias{import,TENxFileList,ANY,ANY-method}

+\alias{metadata,TENxFileList-method}

 \title{TENxFileList: A list-like representation for TENxFiles}

 \usage{

 \S4method{path}{TENxFileList}(object, ...)

@@ -14,6 +15,8 @@

 \S4method{decompress}{TENxFileList}(manager, con, ...)

 \S4method{import}{TENxFileList,ANY,ANY}(con, format, text, ...)

+

+\S4method{metadata}{TENxFileList}(x, ...)

 }

 \arguments{

 \item{object}{

@@ -22,9 +25,7 @@

     number of paths.

   }

-\item{...}{

-    Additional arguments, for use in specific methods.

-  }

+\item{...}{Additional arguments (not used)}

 \item{manager}{A \code{ConnectionManager} internal instance; currently not used.}

@@ -41,6 +42,9 @@ unnecessary when \code{con} is a derivative of \linkS4class{BiocFile}.}

 \item{text}{If \code{con} is missing, this can be a character vector directly

 providing the string data to import.}

+

+\item{x}{An object of class \code{TENxFile}, \code{TENxFileList}, \code{TENxMTX}, \code{TENxH5},

+\code{TENxPeaks}, \code{TENxTSV}, or derivatives}

 }

 \value{

 A \code{TENxFileList} class object

@@ -76,6 +80,8 @@ as a vector

 \item \code{import(con = TENxFileList, format = ANY, text = ANY)}: Recursively import files within a

 \code{TENxFileList}

+\item \code{metadata(TENxFileList)}: \code{metadata} method for \code{TENxFileList} objects

+

 }}

 \section{Slots}{

@@ -59,6 +59,11 @@ identifiers

 Note that version '2' includes \code{genes.tsv.gz} instead of \code{features.tsv.gz} in

 version '3'.

 }

+

+An additional \code{ref} argument can be provided when the file contains

+multiple \code{feature_type} in the file or "Type" in the \code{rowData}. By default,

+the first type reported in \code{table()} is set as the \code{mainExpName} in the

+\code{SingleCellExperiment} object.

 }

 \section{Functions}{

 \itemize{

@@ -28,23 +28,19 @@

 \item{manager}{A \code{ConnectionManager} internal instance; currently not used.}

-\item{con}{ The connection from which data is loaded or to which data

-    is saved. If this is a character vector, it is assumed to be a

-    filename and a corresponding file connection is created and then

-    closed after exporting the object. If a \code{\linkS4class{BiocFile}}

-    derivative, the data is loaded from or saved to the underlying

-    resource. If missing, the function will return the output as a

-    character vector, rather than writing to a connection.

-  }

+\item{con}{The connection from which data is loaded or to which data is

+saved. If this is a \code{character} vector, it is assumed to be a file name and

+a corresponding file connection is created and then closed after exporting

+the object. If it is a \linkS4class{BiocFile} derivative, the data is loaded from

+or saved to the underlying resource. If missing, the function will return

+the output as a character vector, rather than writing to a connection.}

-\item{format}{ The format of the output. If missing and \code{con} is

-    a filename, the format is derived from the file extension. This

-    argument is unnecessary when \code{con} is a derivative of

-    \code{\linkS4class{BiocFile}}.

-  }

+\item{format}{The format of the output. If missing and \code{con} is a

+file name, the format is derived from the file extension. This argument is

+unnecessary when \code{con} is a derivative of \linkS4class{BiocFile}.}

-\item{text}{ If \code{con} is missing, this can be a character vector

-    directly providing the string data to import. }

+\item{text}{If \code{con} is missing, this can be a character vector directly

+providing the string data to import.}

 }

 \value{

 A \code{TENxFileList} class object

@@ -60,6 +60,8 @@ These tarballs usually contain three files:

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

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

 identifiers

+Note that version '2' includes \code{genes.tsv.gz} instead of \code{features.tsv.gz} in

+version '3'.

 }

 }

 \section{Functions}{

@@ -82,5 +82,8 @@ as a vector

 \item{\code{extension}}{character() A vector of file extensions for each file}

 \item{\code{compressed}}{logical(1) Whether the file is compressed as \code{.tar.gz}}

+

+\item{\code{version}}{character(1) The version number of the tarball usually either

+'2' or '3'}

 }}

@@ -46,6 +46,9 @@

 \item{text}{ If \code{con} is missing, this can be a character vector

     directly providing the string data to import. }

 }

+\value{

+A \code{TENxFileList} class object

+}

 \description{

 This class was designed to mainly handle tarballs from

 10X Genomics. The typical file extension for these tarballs is \code{.tar.gz}.

@@ -81,10 +81,3 @@ as a vector

 \item{\code{compressed}}{logical(1) Whether the file is compressed as \code{.tar.gz}}

 }}

-\examples{

-

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

-con <- TENxFileList(fl)

-import(con)

-

-}

@@ -61,16 +61,16 @@ identifiers

 }

 \section{Functions}{

 \itemize{

-\item \code{path,TENxFileList-method}: Obtain file paths for all files in the object

+\item \code{path(TENxFileList)}: Obtain file paths for all files in the object

 as a vector

-\item \code{decompress,TENxFileList-method}: An intermediate method for decompressing

+\item \code{decompress(TENxFileList)}: An intermediate method for decompressing

 (via untar) the contents of a \code{.tar.gz} file list

-\item \code{import,TENxFileList,ANY,ANY-method}: Recursively import files within a

+\item \code{import(con = TENxFileList, format = ANY, text = ANY)}: Recursively import files within a

 \code{TENxFileList}

-}}

+}}

 \section{Slots}{

 \describe{

@@ -26,6 +26,8 @@

     Additional arguments, for use in specific methods.

   }

+\item{manager}{A \code{ConnectionManager} internal instance; currently not used.}

+

 \item{con}{ The connection from which data is loaded or to which data

     is saved. If this is a character vector, it is assumed to be a

     filename and a corresponding file connection is created and then

@@ -25,6 +25,24 @@

 \item{...}{

     Additional arguments, for use in specific methods.

   }

+

+\item{con}{ The connection from which data is loaded or to which data

+    is saved. If this is a character vector, it is assumed to be a

+    filename and a corresponding file connection is created and then

+    closed after exporting the object. If a \code{\linkS4class{BiocFile}}

+    derivative, the data is loaded from or saved to the underlying

+    resource. If missing, the function will return the output as a

+    character vector, rather than writing to a connection.

+  }

+

+\item{format}{ The format of the output. If missing and \code{con} is

+    a filename, the format is derived from the file extension. This

+    argument is unnecessary when \code{con} is a derivative of

+    \code{\linkS4class{BiocFile}}.

+  }

+

+\item{text}{ If \code{con} is missing, this can be a character vector

+    directly providing the string data to import. }

 }

 \description{

 This class was designed to mainly handle tarballs from

@@ -15,6 +15,17 @@

 \S4method{import}{TENxFileList,ANY,ANY}(con, format, text, ...)

 }

+\arguments{

+\item{object}{

+    An object containing paths. Even though it will typically contain

+    a single path, \code{object} can actually contain an arbitrary

+    number of paths.

+  }

+

+\item{...}{

+    Additional arguments, for use in specific methods.

+  }

+}

 \description{

 This class was designed to mainly handle tarballs from

 10X Genomics. The typical file extension for these tarballs is \code{.tar.gz}.

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

 \usage{

 \S4method{path}{TENxFileList}(object, ...)

-\S4method{decompress}{TENxFileList}(object, ...)

+\S4method{decompress}{TENxFileList}(manager, con, ...)

 \S4method{import}{TENxFileList,ANY,ANY}(con, format, text, ...)

 }

@@ -5,9 +5,15 @@

 \alias{TENxFileList-class}

 \alias{.TENxFileList}

 \alias{path,TENxFileList-method}

+\alias{decompress,TENxFileList-method}

+\alias{import,TENxFileList,ANY,ANY-method}

 \title{TENxFileList: A list-like representation for TENxFiles}

 \usage{

 \S4method{path}{TENxFileList}(object, ...)

+

+\S4method{decompress}{TENxFileList}(object, ...)

+

+\S4method{import}{TENxFileList,ANY,ANY}(con, format, text, ...)

 }

 \description{

 This class was designed to mainly handle tarballs from

@@ -18,13 +24,20 @@ 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

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

+identifiers

 }

 }

 \section{Functions}{

 \itemize{

 \item \code{path,TENxFileList-method}: Obtain file paths for all files in the object

 as a vector

+

+\item \code{decompress,TENxFileList-method}: An intermediate method for decompressing

+(via untar) the contents of a \code{.tar.gz} file list

+

+\item \code{import,TENxFileList,ANY,ANY-method}: Recursively import files within a

+\code{TENxFileList}

 }}

 \section{Slots}{

@@ -37,3 +50,10 @@ as a vector

 \item{\code{compressed}}{logical(1) Whether the file is compressed as \code{.tar.gz}}

 }}

+\examples{

+

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

+con <- TENxFileList(fl)

+import(con)

+

+}

new file mode 100644

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

+% Generated by roxygen2: do not edit by hand

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

+\docType{class}

+\name{TENxFileList-class}

+\alias{TENxFileList-class}

+\alias{.TENxFileList}

+\alias{path,TENxFileList-method}

+\title{TENxFileList: A list-like representation for TENxFiles}

+\usage{

+\S4method{path}{TENxFileList}(object, ...)

+}

+\description{

+This class was designed to mainly handle tarballs from

+10X Genomics. The typical file extension for these tarballs is \code{.tar.gz}.

+}

+\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

+}

+}

+\section{Functions}{

+\itemize{

+\item \code{path,TENxFileList-method}: Obtain file paths for all files in the object

+as a vector

+}}

+

+\section{Slots}{

+

+\describe{

+\item{\code{listData}}{list() The data in list format}

+

+\item{\code{extension}}{character() A vector of file extensions for each file}

+

+\item{\code{compressed}}{logical(1) Whether the file is compressed as \code{.tar.gz}}

+}}

+