BachMammaryData: Obtain the Bach mammary data

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

Obtain the Bach mammary data

Description

Obtain the mouse mammary gland single-cell RNA-seq data from Bach et al. (2017).

Usage

BachMammaryData(
  samples = c("NP_1", "NP_2", "G_1", "G_2", "L_1", "L_2", "PI_1", "PI_2"),
  location = TRUE,
  legacy = FALSE
)

Arguments

samples	A character vector with at least one element, specifying which samples(s) to retrieve.
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 is extracted from the sample annotation in GSE106273, and refers to the developmental stage of the mammary gland.

If multiple samples are specified in samples, the count matrices will be cbinded together. Cells originating from different samples are identifiable by the "Sample" field in the column metadata.

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/bach-mammary.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Bach K et al. (2017). Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing. Nat Commun. 8(1), 2128

Examples

sce <- BachMammaryData(samples="NP_1")

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