ChenBrainData: Obtain the Chen brain data

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

Obtain the Chen brain data

Description

Obtain the mouse brain single-cell RNA-seq data from Chen et al. (2017).

Usage

ChenBrainData(ensembl = FALSE, location = TRUE, legacy = FALSE)

Arguments

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 GSE87544. This contains the putative cell type assigned by the original authors.

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/chen-brain.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Chen R et al. (2017). Single-Cell RNA-Seq reveals hypothalamic cell diversity. Cell Rep. 18, 3227-3241.

Examples

sce <- ChenBrainData()

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