ShekharRetinaData: Obtain the Shekhar retina data

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

Obtain the Shekhar retina data

Description

Obtain the mouse retina single-cell RNA-seq dataset from Shekhar et al. (2016).

Usage

ShekharRetinaData(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 contains the cluster identities as reported in the paper. Note that some cells will have NA identities as they are present in the count matrix but not in the metadata file. These are presumably low-quality cells that were discarded prior to clustering.

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/shekhar-retina.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Shekhar K et al. (2016). Comprehensive classification of retinal bipolar neurons by single-cell transcriptomics. Cell 166(5), 1308-1323.

Examples

sce <- ShekharRetinaData()

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