R/importCellRanger.R
importCellRangerV2Sample.Rd
Read the filtered barcodes, features, and matrices for all samples from Cell Ranger V2 output. Files are assumed to be named "matrix.mtx", "genes.tsv", and "barcodes.tsv".
importCellRangerV2Sample( dataDir = NULL, sampleName = NULL, class = c("Matrix", "matrix"), delayedArray = FALSE )
dataDir | A path to the directory containing the data files. Default "./". |
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sampleName | A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample". |
class | Character. The class of the expression matrix stored in the SCE object. Can be one of "Matrix" (as returned by readMM function), or "matrix" (as returned by matrix function). Default "Matrix". |
delayedArray | Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default |
A SingleCellExperiment
object containing the count
matrix, the feature annotations, and the cell annotation for the sample.
sce <- importCellRangerV2Sample( dataDir = system.file("extdata/pbmc_4k_v2_20x20/outs/", "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"), sampleName = "pbmc4k_20")