ErnstSpermatogenesisData: Obtain the Ernst spermatogenesis data

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

Obtain the Ernst spermatogenesis data

Description

Obtain the mouse spermatogenesis single-cell RNA-seq dataset from Ernst et al. (2019).

Usage

ErnstSpermatogenesisData(
  method = c("emptyDrops", "Cellranger"),
  location = TRUE,
  legacy = FALSE
)

Arguments

method	String indicating which cell caller to obtain results for.
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

This study contains two analyses done with datasets from different cell calling algorithms. One uses Cellranger version 2 while the other uses emptyDrops from DropletUtils.

Column metadata includes sample information, per-cell QC metrics and cell type labels. In particular, the sample label specifies the developmental stage of the mouse.

Note that method="Cellranger" contains additional data for Tc1 mice. These mice have an additional human chromosome 21 inserted alongside the usual mouse chromosomes.

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/ernst-spermatogenesis.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Ernst C et al. (2019). Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis. Nat Commun 10, 1251

Examples

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

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