BhaduriOrganoidData: Obtain the Bhaduri cortical organoid data

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

Obtain the Bhaduri cortical organoid data

Description

Obtain the human cortical organoid single-cell RNA-seq dataset from Bhaduri et al. (2020).

Usage

BhaduriOrganoidData(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 data contains sample-level information. In theory, there is also cell-level metadata for this dataset but it could not be unambiguously mapped to the column names.

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/bhaduri-organoid.

Value

A SingleCellExperiment object with a single matrix of normalized expression values.

Author(s)

Aaron Lun

References

Bhaduri A et al. (2020). Cell stress in cortical organoids impairs molecular subtype specification. Nature 578(7793), 142-148.

Examples

if (.Machine$sizeof.pointer > 4) { # too large for 32-bit machines!
    sce <- BhaduriOrganoidData()
}

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