read10xCounts {DropletUtils} | R Documentation

## Load in data from 10x experiment

### Description

Creates a SingleCellExperiment from the CellRanger output directories for 10X Genomics data.

### Usage

    read10xCounts(samples, col.names=FALSE, ...)

### Arguments

`samples` | A character vector containing one or more directory names, each corresponding to a 10X sample. Each directory should contain the `"matrix.mtx"`, `"genes.tsv"` and `"barcodes.tsv"` files generated by CellRanger.
`col.names` | A logical scalar indicating whether the columns of the output object should be named with the cell barcodes.
`...` | Further arguments to pass to `read10xMatrix`.

### Details

This function was originally developed from the `Read10X` function from the Seurat package. It was then taken from the `read10xResults` implementation in the scater package.

If `col.names=TRUE` and `length(sample)==1`, each column is named by the cell barcode. For multiple samples, the columns are unnamed to avoid problems with non-unique barcodes across samples.

Note that user-level manipulation of sparse matrices requires loading of the Matrix package. Otherwise, calculation of `rowSums`, `colSums`, etc. will result in errors.

### Value

A SingleCellExperiment object with counts data stored as a sparse matrix. Matrices are combined by column if multiple `samples` were specified. Rows are named with the gene identifier (usually ENSEMBL).

### Author(s)

Davis McCarthy, with modifications from Aaron Lun

### References

Zheng GX, Terry JM, Belgrader P, and others (2017). Massively parallel digital transcriptional profiling of single cells. Nat Commun 8:14049.

10X Genomics (2017). Gene-Barcode Matrices. https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/matrices

### See Also

`write10xCounts`

### Examples

    # Mocking up some 10X genomics output.
    example(write10xCounts)

    # Reading it in.
    sce10x <- read10xCounts(tmpdir)

    # Column names are dropped with multiple 'samples'.
    sce10x2 <- read10xCounts(c(tmpdir, tmpdir))

[Package DropletUtils version 1.0.3 Index]