read10X {edgeR} | R Documentation

## Read 10X Genomics Files

### Description

Reads 10X Genomics files containing single-cell RNA-seq UMI counts in Matrix Market format.

### Usage

    read10X(mtx = NULL, genes = NULL, barcodes = NULL, path = ".", DGEList = TRUE)

### Arguments

`mtx` | name of `mtx` file containing counts in Matrix Exchange Format. Defaults to `matrix.mtx` or `matrix.mtx.gz`.
`genes` | name of file containing gene IDs and names. Defaults to `features.tsv` or `genes.tsv` or gzipped versions of the same.
`barcodes` | optional name of file containing barcodes. Defaults to `"barcodes.tsv"` or `barcodes.tsv.gz`.
`path` | character string giving the directory containing the files. Defaults to the current working directory.
`DGEList` | logical. If `TRUE`, a `DGEList` will be returned, otherwise an unclassed list is returned.

### Details

This function reads output files created by the 10X Genomics Cellranger pipeline, see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices. The UMI counts are assembled into an integer matrix in R with accompanying gene IDs and gene symbols. The results are returned as either a `DGEList` or an ordinary list.

The files `mtx`, `genes` and `barcodes` can be provided in either gzipped or unzipped versions.

This function creates an ordinary matrix of counts. To read the counts instead into a sparse matrix format, the `read10xResults` function in the scater package is an alternative.

### Value

Either a `DGEList` object (if `DGEList=TRUE`) or an ordinary list with the following components:

`counts` | matrix of counts.
`genes` | data.frame counting gene symbols.
`samples` | data.frame containing information about each cell. This will be omitted if `barcodes=NULL` and `DGEList=FALSE`.

The only difference between the `DGEList` or list formats is that the `DGEList` adds some extra columns to the `samples` data.frame.

### Author(s)

Gordon Smyth

### See Also

`read10xResults` in the scater package.

### Examples

    ## Not run:
    GEO <- "ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2510nnn/GSM2510617/suppl/"
    GEOmtx <- paste0(GEO,"GSM2510617_P7-matrix.mtx.gz")
    GEOgenes <- paste0(GEO,"GSM2510617_P7-genes.tsv.gz")
    download.file(GEOmtx,"matrix.mtx.gz")
    download.file(GEOgenes,"genes.tsv.gz")
    y <- read10X("matrix.mtx.gz", "genes.tsv.gz")

    ## End(Not run)

[Package edgeR version 3.28.1 Index]