MuraroPancreasData: Obtain the Muraro pancreas data

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

Obtain the Muraro pancreas data

Description

Obtain the human pancreas single-cell RNA-seq data from Muraro et al. (2016).

Usage

MuraroPancreasData(ensembl = FALSE, location = TRUE, legacy = FALSE)

Arguments

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

Row data contains fields for the symbol and chromosomal location of each gene.

Column metadata is derived from the columns of the count matrix provided in GSE85241, with additional cell type labels obtained from the authors (indirectly, via the Hemberg group). Some cells have NA labels and were presumably removed prior to downstream analyses.

Count data for ERCC spike-ins are stored in the "ERCC" entry of the altExps.

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/muraro-pancreas.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun, using additional metadata obtained by Vladimir Kiselev.

References

Muraro MJ et al. (2016). A single-cell transcriptome atlas of the human pancreas. Cell Syst. 3(4), 385-394.

Examples

sce <- MuraroPancreasData()

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