importCellRangerV2Sample {singleCellTK} | R Documentation

## Construct SCE object from Cell Ranger V2 output for a single 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".

### Usage

    importCellRangerV2Sample(
      dataDir = NULL,
      sampleName = NULL,
      class = c("Matrix", "matrix"),
      delayedArray = FALSE
    )

### 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`.

### 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")

[Package singleCellTK version 2.2.0 Index]