DarmanisBrainData: Obtain the Darmanis brain data

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

Obtain the Darmanis brain data

Description

Obtain the human brain single-cell RNA-seq dataset from Darmanis et al. (2015).

Usage

DarmanisBrainData(
  ensembl = FALSE,
  location = TRUE,
  remove.htseq = 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.
remove.htseq	Logical scalar indicating whether HT-seq alignment statistics should be removed.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

Column metadata is scraped from GEO and includes patient information, tissue of origin and likely cell type.

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. This is only performed when ensembl=TRUE.

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

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

Darmanis S et al. (2015). A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci USA 112, 7285-90.

Examples

sce <- DarmanisBrainData()

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.