NestorowaHSCData: Obtain the Nestorowa HSC data

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

Obtain the Nestorowa HSC data

Description

Obtain the mouse haematopoietic stem cell single-cell RNA-seq data from Nestorowa et al. (2015).

Usage

NestorowaHSCData(remove.htseq = TRUE, location = TRUE, legacy = FALSE)

Arguments

remove.htseq	Logical scalar indicating whether HT-seq alignment statistics should be removed.
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

Rows corresponding to HT-seq's alignment statistics are removed by default. These can be retained by setting remove.htseq=FALSE.

Column metadata includes the cell type mapping, as described on the website (see References), and the FACS expression levels of selected markers. Note that these are stored as nested matrices within the colData.

Diffusion map components are provided as the "diffusion" entry in the reducedDims.

Counts for ERCC spike-ins are stored in the "ERCC" entry in the altExps.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output.

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

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Nestorowa S et al. (2016). A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation Blood 128, e20-e31.

Gene and protein expression in adult haematopoiesis: Data. http://blood.stemcells.cam.ac.uk/single_cell_atlas.html#data.

Examples

sce <- NestorowaHSCData()

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