NowakowskiCortexData: Obtain the Nowakowski cortex data

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

Obtain the Nowakowski cortex data

Description

Obtain the human cortex single-cell RNA-seq dataset from Nowakowski et al. (2017).

Usage

NowakowskiCortexData(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 includes the presumed cell type (WGCNAcluster), patient and tissue region of origin. A variety of dimensionality reduction results are also provided.

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. This is only performed when ensembl=TRUE.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/nowakowski-cortex.

Value

A SingleCellExperiment object with a single matrix of TPMs. The reducedDims contains an assortment of dimensionality reduction results.

Author(s)

Aaron Lun

References

Nowakowski S et al. (2017). Spatiotemporal gene expression trajectories reveal developmental hierarchies of the human cortex. Science 358, 1318-1323.

Examples

sce <- NowakowskiCortexData()

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