BaronPancreasData: Obtain the Baron pancreas data

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain the Baron pancreas data

Description

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

Usage

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

Arguments

which	String specifying the species to get data for.
ensembl	Logical scalar indicating whether the output row names should contain Ensembl identifiers.
location	Logical scalar indicating whether genomic coordinates should be returned.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

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.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output. Note that this is only performed if ensembl=TRUE.

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

sce.human <- BaronPancreasData()

sce.mouse <- BaronPancreasData("mouse")

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.