RomanovBrainData: Obtain the Romanov brain data

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

Obtain the Romanov brain data

Description

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

Usage

RomanovBrainData(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 GSE74672. This contains information such as the reporter gene expressed in each cell, the mouse line, dissection type and so on.

Counts for ERCC spike-ins are stored in the "ERCC" entry of the altExps. Note that some of the spike-in rows have NA observations for some (but not all) cells.

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/romanov-brain.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun, based on code by Vladimir Kiselev and Tallulah Andrews.

References

Romanov RA et al. (2017). Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes. Nat. Neurosci. 20, 176-188.

Examples

sce <- RomanovBrainData()

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.