BaronPancreasData: Obtain the Baron pancreas data

Description Usage Arguments Details Value Author(s) References Examples

View source: R/BaronPancreasData.R

Description

Obtain the human/mouse pancreas single-cell RNA-seq data from Baron et al. (2017).

Usage

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BaronPancreasData(which = c("human", "mouse"), ensembl = FALSE)

Arguments

which

String specifying the species to get data for.

ensembl

Logical scalar indicating whether the output row names should contain Ensembl identifiers.

Details

Column metadata is provided in the same form as supplied in GSE84133. This contains information such as the cell type labels and donor ID (for humans) or strain (for mouse).

If ensembl=TRUE, the gene symbols are converted to Ensembl IDs in the row names of the output object. Rows with missing Ensembl IDs are discarded, and only the first occurrence of duplicated IDs is retained.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/baron-pancreas.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Baron M et al. (2017). Single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Cell Syst. 3(4), 346-360.

Examples

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sce.human <- BaronPancreasData()

sce.mouse <- BaronPancreasData("mouse")

LTLA/scRNAseq documentation built on Nov. 13, 2019, 12:43 p.m.