read10xResults {scater} | R Documentation |
Creates a full or sparse matrix from a sparse data matrix provided by 10X genomics.
read10xResults(data_dir, min_total_cell_counts = NULL, min_mean_gene_counts = NULL) read10XResults(...)
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 |
This function calls read10xCounts
from the DropletUtils package. It is deprecated and will be removed
in the next release.
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).
sce10x <- read10xResults(system.file("extdata", package="scater"))