importExampleData {singleCellTK} | R Documentation

## Retrieve example datasets

### Description

Retrieves published example datasets stored in SingleCellExperiment using the scRNAseq and TENxPBMCData packages. See 'Details' for a list of available datasets.

### Usage

    importExampleData(dataset, class = c("Matrix", "matrix"), delayedArray = FALSE)

### Arguments

`dataset` | Character. Name of the dataset to retrieve.
`class` | Character. The class of the expression matrix stored in the SCE object. Can be one of `"Matrix"` or `"matrix"`. `"Matrix"` will store the data as a sparse matrix from package Matrix while `"matrix"` will store the data in a standard matrix. Default `"Matrix"`.
`delayedArray` | Boolean. Whether to read the expression matrix as DelayedArray object or not. Default `FALSE`.

### Details

See the list below for the available datasets and their descriptions.

"fluidigm_pollen"

  Retrieved with `ReprocessedFluidigmData`. Returns a dataset of 65 human neural cells from Pollen et al. (2014), each sequenced at high and low coverage (SRA accession SRP041736).

"allen_tasic"

  Retrieved with `ReprocessedAllenData`. Returns a dataset of 379 mouse brain cells from Tasic et al. (2016).

"pbmc3k"

  Retrieved with `TENxPBMCData`. 2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

"pbmc4k"

  Retrieved with `TENxPBMCData`. 4,340 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

"pbmc6k"

  Retrieved with `TENxPBMCData`. 5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

"pbmc8k"

  Retrieved with `TENxPBMCData`. 8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

"pbmc33k"

  Retrieved with `TENxPBMCData`. 33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

"pbmc68k"

  Retrieved with `TENxPBMCData`. 68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.

### Value

The specified SingleCellExperiment object.

### Author(s)

Joshua D. Campbell, David Jenkins

### Examples

    sce <- importExampleData("pbmc3k")

[Package singleCellTK version 2.0.0 Index]