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]