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,
rowNamesDedup = TRUE
)
A path to the directory containing the data files. Default "./".
A User-defined sample name. This will be prepended to all cell barcode IDs. Default "sample".
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".
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default FALSE
.
Boolean. Whether to deduplicate rownames. Default
TRUE
.
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")
#> Metrics summary file (metrics_summary.csv) not found for sample: pbmc4k_20