importCellRangerV3Sample: Construct SCE object from Cell Ranger V3 output for a single...

Description Usage Arguments Value Examples

View source: R/importCellRanger.R

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

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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

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

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.