Read10X function

Load in data from 10X

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 )

Arguments

  • 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.

Returns

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.

Examples

## 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)
  • Maintainer: Rahul Satija
  • License: MIT + file LICENSE
  • Last published: 2024-05-10