read10X: Read 10X Genomics Files
In edgeR: Empirical Analysis of Digital Gene Expression Data in R

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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.

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.

Gordon Smyth

read10xResults in the scater package.

## 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)