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]