TENxMTX: Represent Matrix Market Format Files from 10X

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)
#> class: SummarizedExperiment 
#> dim: 171 10 
#> metadata(1): TENxFile
#> assays(1): counts
#> rownames: NULL
#> rowData names(0):
#> colnames: NULL
#> colData names(0):