UsoskinBrainData: Obtain the Usoskin brain data

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

Obtain the Usoskin brain data

Description

Obtain the mouse brain single-cell RNA-seq dataset from Usoskin et al. (2015).

Usage

UsoskinBrainData(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 External Table 2 of http://linnarssonlab.org/drg/. This contains information such as the library of origin and the cell type.

The count matrix contains information for repeats, marked with r_ prefixes in the row names; as well as mitochondrial transcripts, marked with mt- prefixes.

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/usoskin-brain.

Value

A SingleCellExperiment object with a single matrix of RPMs.

Author(s)

Aaron Lun

References

Usoskin A et al. (2015). Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat. Neurosci. 18(1), 145-53.

Examples

sce <- UsoskinBrainData()

LTLA/scRNAseq documentation built on April 14, 2024, 7:13 a.m.