GrunHSCData: Obtain the Grun HSC data

Description Usage Arguments Details Value Author(s) References Examples

View source: R/GrunHSCData.R

Description

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

Usage

1
GrunHSCData(ensembl = FALSE)

Arguments

ensembl

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

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.

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

1
sce <- GrunHSCData()

LTLA/scRNAseq documentation built on Nov. 13, 2019, 12:43 p.m.