read10xMatrix {DropletUtils}R Documentation

Read in the 10x count matrix

Description

Creates a sparse or HDF5-backed count matrix from the MatrixMarket file produced by CellRanger.

Usage

read10xMatrix(file, hdf5.out=FALSE, chunk.size)

Arguments

file

String containing the path to a MatrixMarket file, usually named "matrix.mtx".

hdf5.out

A logical scalar indicating whether a HDF5Matrix object should be produced.

chunk.size

An integer scalar specifying the chunk size when reading in records from file.

Details

When hdf5.out=FALSE, readMM is used directly. However, for very large 10x experiments with more than .Machine$integer.max non-zero entries, dgCMatrix may encounter integer overflows. In such cases, setting hdf5.out=TRUE will produce a HDF5Matrix object instead.

Value

A dgCMatrix object (or a HDF5Matrix object, if hdf5.out=TRUE) containing the counts for each gene (row) and cell barcode (column).

Author(s)

Aaron Lun

References

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

See Also

readMM, read10xCounts

Examples

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

mm.path <- file.path(tmpdir, "matrix.mtx")
X <- read10xMatrix(mm.path)
altX <- read10xMatrix(mm.path, chunk.size=10, hdf5.out=TRUE)

[Package DropletUtils version 1.0.3 Index]