WuKidneyData: Obtain the Wu kidney data

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

Obtain the Wu kidney data

Description

Obtain the mouse kidney single-nuclei RNA-seq data from Wu et al. (2019).

Usage

WuKidneyData(
  mode = c("healthy", "disease"),
  ensembl = FALSE,
  location = TRUE,
  legacy = FALSE
)

Arguments

mode	String indicating whether to return data for healthy and/or diseased donors.
ensembl	Logical scalar indicating whether the output row names should contain Ensembl identifiers.
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 single-cell technology and whether they came from a diseased or healthy individual.

If mode specifies both healthy and disease donors, counts are only reported for the intersection of genes that are present for both donors. This is because the original count matrices had differences in their annotation.

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/wu-kidney.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Wu H et al. (2019). Advantages of single-nucleus over single-cell RNA sequencing of adult kidney: rare cell types and novel cell states revealed in fibrosis. J. Am. Soc. Nephrol. 30, 23-32.

Examples

sce <- WuKidneyData("disease")

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