ZhaoImmuneLiverData: Obtain the Zhao immune liver data

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

Obtain the Zhao immune liver data

Description

Obtain the human liver immune single-cell RNA-seq data from Zhao et al. (2020).

Usage

ZhaoImmuneLiverData(location = TRUE, filter = FALSE, legacy = FALSE)

Arguments

location	Logical scalar indicating whether genomic coordinates should be returned.
filter	Logical scalar indicating if the filtered subset 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 contains various cell labels as provided by the authors. Some of these labels required assembly on our part:

• The broad label was assigned to each barcode based on whether that barcode was present in each *_identities.tsv.gz in GSE125188's supplementary files.

• For each cell barcode that was present in one of these files, the fine label was generated from the Group annotations inside that file.

We guessed the sample for each cell by assuming that the GEM group numbers match the order of samples in GSE125188. We also assumed that “donor 4” is a typo, given that the paper only mentions 3 donors.

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.

If filter=TRUE, only cells that have been used in the original analysis are returned. Otherwise, the cells used are specified in the retained column of the colData.

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

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Zhao J et al. (2020). Single-cell RNA sequencing reveals the heterogeneity of liver-resident immune cells in human. Cell Discov 6, 22.

Examples

sce.zhao <- ZhaoImmuneLiverData()

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