R/importCellRanger.R
importCellRangerV3Sample.Rd
Read the filtered barcodes, features, and matrices for all samples from Cell Ranger V3 output. Files are assumed to be named "matrix.mtx.gz", "features.tsv.gz", and "barcodes.tsv.gz".
importCellRangerV3Sample( dataDir = "./", sampleName = "sample", 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 <- importCellRangerV3Sample( dataDir = system.file("extdata/hgmm_1k_v3_20x20/outs/", "filtered_feature_bc_matrix", package = "singleCellTK"), sampleName = "hgmm1kv3")