% 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}

 \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, ...)

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

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

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

 }

 \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 (not used)}

 \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 \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 \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 \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.}

 
 \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
 }

 \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

 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{

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

 as a vector

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

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

 \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}{
 
 \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}}

 
 \item{\code{version}}{character(1) The version number of the tarball usually either
 '2' or '3'}

 }}