MarquesBrainData: Obtain the Marques brain data

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

Obtain the Marques brain data

Description

Obtain the mouse brain single-cell RNA-seq data from Marques et al. (2016).

Usage

MarquesBrainData(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 GSE75330. This contains information such as the cell type and age/sex of the mouse of origin for each cell.

Note that some genes may be present in multiple rows corresponding to different genomic locations. These additional rows are identified by a _loc[2-9] suffix in their row names. Users may wish to consider either removing them or merging them, e.g., with scater::sumCountsAcrossFeatures.

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. All searching is performed after removing the _loc[2-9] suffix.

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/marques-brain.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Marques A et al. (2016). Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system. Science 352(6291), 1326-1329.

Examples

sce <- MarquesBrainData()

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