TENxMTX: TENxMTX: Represent Matrix Market Format Files from 10X

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

TENxMTX: Represent Matrix Market Format Files from 10X

Description

This constructor function accepts .mtx and .mtx.gz compressed formats for eventual importing. It is mainly used with tarball files from 10X Genomics, where more annotation data is included. Importing solely the .mtx format will provide users with a SummarizedExperiment with an assay of class dgCMatrix from the Matrix package. Currently, other formats are not supported but if you'd like to request support for a format, please open an issue on GitHub.

Usage

TENxMTX(resource, compressed = FALSE, ...)

Arguments

resource	character(1) The path to the file
compressed	logical(1) Whether the resource file is compressed (default FALSE)
...	Additional inputs to the low level class generator functions

Value

A SummarizedExperiment instance with a dgCMatrix in the assay

Examples

mtxf <- system.file(
    "extdata", "pbmc_3k_ff_bc_ex.mtx",
    package = "TENxIO", mustWork = TRUE
)

con <- TENxMTX(mtxf)

import(con)

LiNk-NY/TENxIO documentation built on Nov. 16, 2024, 7:10 p.m.