RichardTCellData: Obtain the Richard T cell data

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

Obtain the Richard T cell data

Description

Obtain the mouse CD8+ T cell single-cell RNA-seq data from Richard et al. (2018).

Usage

RichardTCellData(location = TRUE, legacy = FALSE)

Arguments

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 E-MTAB-6051. This contains information such as the stimulus, time after stimulation, age of the mice and sequencing batch.

Count data for ERCC spike-ins are stored in the "ERCC" entry of the altExps.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output.

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

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Richard AC et al. (2018). T cell cytolytic capacity is independent of initial stimulation strength. Nat. Immunol. 19(8), 849-858.

Examples

sce <- RichardTCellData()

LTLA/scRNAseq documentation built on April 19, 2024, 10:36 a.m.