Load in data from 10X
Enables easy loading of sparse data matrices provided by 10X genomics.
Read10X( data.dir, gene.column = 2, cell.column = 1, unique.features = TRUE, strip.suffix = FALSE )
data.dir |
Directory containing the matrix.mtx, genes.tsv (or features.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. |
gene.column |
Specify which column of genes.tsv or features.tsv to use for gene names; default is 2 |
cell.column |
Specify which column of barcodes.tsv to use for cell names; default is 1 |
unique.features |
Make feature names unique (default TRUE) |
strip.suffix |
Remove trailing "-1" if present in all cell barcodes. |
If features.csv indicates the data has multiple data types, a list containing a sparse matrix of the data from each type will be returned. Otherwise a sparse matrix containing the expression data will be returned.
## Not run: # For output from CellRanger < 3.0 data_dir <- 'path/to/data/directory' list.files(data_dir) # Should show barcodes.tsv, genes.tsv, and matrix.mtx expression_matrix <- Read10X(data.dir = data_dir) seurat_object = CreateSeuratObject(counts = expression_matrix) # For output from CellRanger >= 3.0 with multiple data types data_dir <- 'path/to/data/directory' list.files(data_dir) # Should show barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz data <- Read10X(data.dir = data_dir) seurat_object = CreateSeuratObject(counts = data$`Gene Expression`) seurat_object[['Protein']] = CreateAssayObject(counts = data$`Antibody Capture`) ## End(Not run)
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