TENxFileList-class: TENxFileList: A list-like representation for TENxFiles

In LiNk-NY/TENxIO: Import methods for 10X Genomics files

TENxFileList: A list-like representation for TENxFiles

Description

This class was designed to mainly handle tarballs from 10X Genomics. The typical file extension for these tarballs is .tar.gz.

Usage

## S4 method for signature 'TENxFileList'
path(object, ...)

## S4 method for signature 'TENxFileList'
decompress(manager, con, ...)

## S4 method for signature 'TENxFileList,ANY,ANY'
import(con, format, text, ...)

Arguments

object	An object containing paths. Even though it will typically contain a single path, object can actually contain an arbitrary number of paths.
...	Additional arguments, for use in specific methods.
manager	A ConnectionManager internal instance; currently not used.
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 file name and a corresponding file connection is created and then closed after exporting the object. If it is a 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.
format	The format of the output. If missing and con is a file name, the format is derived from the file extension. This argument is unnecessary when con is a derivative of BiocFile.
text	If con is missing, this can be a character vector directly providing the string data to import.

Details

These tarballs usually contain three files:

1. matrix.mtx.gz - the counts matrix

2. features.tsv.gz - row metadata usually represented as rowData

3. barcodes.tsv.gz - column names corresponding to cell barcode identifiers Note that version '2' includes genes.tsv.gz instead of features.tsv.gz in version '3'.

Value

A TENxFileList class object

Functions

• path(TENxFileList): Obtain file paths for all files in the object as a vector

• decompress(TENxFileList): An intermediate method for decompressing (via untar) the contents of a .tar.gz file list

• import(con = TENxFileList, format = ANY, text = ANY): Recursively import files within a TENxFileList

Slots

listData

list() The data in list format

extension

character() A vector of file extensions for each file

compressed

logical(1) Whether the file is compressed as .tar.gz

version

character(1) The version number of the tarball usually either '2' or '3'

LiNk-NY/TENxIO documentation built on May 3, 2024, 11:08 p.m.