importExampleData: Retrieve example datasets

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

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,
  rowNamesDedup = TRUE
)

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.
rowNamesDedup	Boolean. Whether to deduplicate rownames. Default TRUE.

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).

"NestorowaHSCData"

Retrieved with NestorowaHSCData. Returns a dataset of 1920 mouse haematopoietic stem cells from Nestorowa et al. 2015

"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")

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