importCellRangerV3Sample {singleCellTK} | R Documentation

## Construct SCE object from Cell Ranger V3 output for a single sample

### Description

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".

### Usage

    importCellRangerV3Sample(
      dataDir = "./",
      sampleName = "sample",
      class = c("Matrix", "matrix"),
      delayedArray = 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 `TRUE`.

### Value

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

### Examples

    sce <- importCellRangerV3Sample(
        dataDir = system.file("extdata/hgmm_1k_v3_20x20/outs/",
            "filtered_feature_bc_matrix", package = "singleCellTK"),
        sampleName = "hgmm1kv3")

[Package singleCellTK version 2.0.0 Index]