importCellRangerV2Sample: Construct SCE object from Cell Ranger V2 output for a single...

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

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,
  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")

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.