read10xResults {scater}R Documentation

Load in data from 10x experiment

Description

Creates a full or sparse matrix from a sparse data matrix provided by 10X genomics.

Usage

read10xResults(data_dir, min_total_cell_counts = NULL,
  min_mean_gene_counts = NULL)

read10XResults(...)

Arguments

data_dir

Directory containing the matrix.mtx, genes.tsv, and barcodes.tsv files provided by 10x. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name.

min_total_cell_counts

integer(1) threshold such that cells (barcodes) with total counts below the threshold are filtered out

min_mean_gene_counts

numeric(1) threshold such that genes with mean counts below the threshold are filtered out.

...

passed arguments

Details

This function calls read10xCounts from the DropletUtils package. It is deprecated and will be removed in the next release.

Value

Returns an SingleCellExperiment object with counts data stored as a sparse matrix. Rows are named with the gene name and columns are named with the cell barcode (if data_dir contains one element; otherwise the columns are unnamed to avoid problems with non-unique barcodes).

Examples

sce10x <- read10xResults(system.file("extdata", package="scater"))


[Package scater version 1.8.4 Index]