PaulHSCData: Obtain the Paul HSC data

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

Obtain the Paul HSC data

Description

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

Usage

PaulHSCData(
  ensembl = FALSE,
  discard.multiple = TRUE,
  location = TRUE,
  legacy = FALSE
)

Arguments

ensembl	Logical scalar indicating whether the output row names should contain Ensembl identifiers.
discard.multiple	Logical scalar indicating whether ambiguous rows should be discarded.
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 metadata includes the plate and the mouse of origin, fluoresence intensities from indexed sorting and the number of cells in each well.

Some of the original rownames are concatenated symbols from multiple genes. We consider these rows to represent ambiguously assigned counts and discard them if discard.multiple=TRUE.

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/nestorowa-hsc.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Paul F et al. (2015). Transcriptional heterogeneity and lineage commitment in myeloid progenitors. Cell 163, 1663-77.

Examples

sce <- PaulHSCData()

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.