Construct SCE object from Cell Ranger V2 output for a single sample

Source: R/importCellRanger.R

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
)

Arguments

dataDir

A path to the directory containing the data files. Default "./".
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 FALSE.
rowNamesDedup

Boolean. Whether to deduplicate rownames. Default TRUE.

Value

A SingleCellExperiment object containing the count matrix, the feature annotations, and the cell annotation for the sample.

Examples

sce <- importCellRangerV2Sample(
    dataDir = system.file("extdata/pbmc_4k_v2_20x20/outs/",
        "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),
    sampleName = "pbmc4k_20")