% Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/importCellRanger.R
 \name{importCellRangerV2Sample}
 \alias{importCellRangerV2Sample}
 \title{Construct SCE object from Cell Ranger V2 output for a single sample}
 \usage{

 importCellRangerV2Sample(

   dataDir = NULL,

   sampleName = NULL,
   class = c("Matrix", "matrix"),

   delayedArray = FALSE,
   rowNamesDedup = TRUE

 )

 }
 \arguments{

 \item{dataDir}{A path to the directory containing the data files. Default "./".}

 
 \item{sampleName}{A User-defined sample name. This will be prepended to all cell barcode IDs.
 Default "sample".}
 
 \item{class}{Character. The class of the expression matrix stored in the SCE
 object. Can be one of "Matrix" (as returned by

 \link{readMM} function), or "matrix" (as returned by

 \link[base]{matrix} function). Default "Matrix".}
 
 \item{delayedArray}{Boolean. Whether to read the expression matrix as

 \link{DelayedArray} object or not. Default \code{FALSE}.}

 
 \item{rowNamesDedup}{Boolean. Whether to deduplicate rownames. Default 
 \code{TRUE}.}

 }
 \value{
 A \code{SingleCellExperiment} object containing the count
  matrix, the feature annotations, and the cell annotation for the sample.
 }
 \description{
 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".
 }

 \examples{
 sce <- importCellRangerV2Sample(

     dataDir = system.file("extdata/pbmc_4k_v2_20x20/outs/",

         "filtered_gene_bc_matrices/GRCh38", package = "singleCellTK"),

     sampleName = "pbmc4k_20")

 }