GrunHSCData: Obtain the Grun HSC data

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

Obtain the Grun HSC data

Description

Obtain the mouse haematopoietic stem cell single-cell RNA-seq data from Grun et al. (2016).

Usage

GrunHSCData(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

Row metadata contains the symbol and chromosomal location for each gene. Column metadata contains the extraction protocol used for each sample, as described in GSE76983.

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/grun-hsc.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Grun D et al. (2016). De novo prediction of stem cell identity using single-cell transcriptome data. Cell Stem Cell 19(2), 266-277.

Examples

sce <- GrunHSCData()

LTLA/scRNAseq documentation built on April 29, 2024, 12:34 p.m.