TasicBrainData: Obtain the Tasic brain data

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

Obtain the Tasic brain data

Description

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

Usage

TasicBrainData(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 GSE71585. This contains information such as the reporter gene expressed in each cell, the mouse line, dissection type and so on.

Count data 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.

The last 9 columns (containing _CTX_ in their names) correspond to no-cell control libraries.

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/tasic-brain.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Tasic A et al. (2016). Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nat. Neurosci. 19(2), 335-46.

Examples

sce <- TasicBrainData()

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