CampbellBrainData: Obtain the Campbell brain data

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

Obtain the Campbell brain data

Description

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

Usage

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

Arguments

ensembl	Logical scalar indicating whether the row names of the returned object 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 GSE93374. This contains information such as the diet of the mice, sex and proposed cell type for each cell.

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/campbell-brain.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Campbell R et al. (2017). A molecular census of arcuate hypothalamus and median eminence cell types. Nat. Neurosci. 20, 484-496.

Examples

sce <- CampbellBrainData()

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