ZhongPrefrontalData: Obtain the Zhong prefrontal cortex data

Description Usage Arguments Details Value Author(s) References Examples

View source: R/ZhongPrefrontalData.R

Description

Obtain the human prefrontal cortex single-cell RNA-seq dataset from Zhong et al. (2018).

Usage

1
ZhongPrefrontalData(ensembl = FALSE, location = TRUE)

Arguments

ensembl

Logical scalar indicating whether the output row names should contain Ensembl identifiers.

location

Logical scalar indicating whether genomic coordinates should be returned.

Details

Column metadata is scraped from GEO and includes week of gestation, gender and likely cell type.

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/zhong-prefrontal.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Zhong S et al. (2018). A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. Nature 555, 524-528.

Examples

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drisso/scRNAseq documentation built on Feb. 16, 2021, 1:18 a.m.