TENxMTX-class: TENxMTX: The Matrix Market representation class for 10X Data

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

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.

Usage

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

Arguments

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.
...	Parameters to pass to the format-specific method.

Details

The TENxMTX class is a straightforward implementation that allows the user to import a Matrix Market file format using Matrix::readMM. Currently, it returns a SummarizedExperiment with an internal dgCMatrix assay. To request other formats, please open an issue on GitHub.

Value

A TENxMTX class object

Methods (by generic)

• import(con = TENxMTX, format = ANY, text = ANY): Import method mainly for mtx.gz files from 10x

Slots

compressed

logical(1) Whether or not the file is in compressed format, usually gzipped (.gz).

LiNk-NY/TENxIO documentation built on Dec. 6, 2024, 8:38 a.m.