LaMannoBrainData: Obtain the La Manno brain data

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

Obtain the La Manno brain data

Description

Obtain the mouse/human brain scRNA-seq data from La Manno et al. (2016).

Usage

LaMannoBrainData(
  which = c("human-es", "human-embryo", "human-ips", "mouse-adult", "mouse-embryo"),
  ensembl = FALSE,
  location = TRUE,
  legacy = FALSE
)

Arguments

which	A string specifying which dataset should be obtained.
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 is provided in the same form as supplied in the supplementary tables in GSE71585. This contains information such as the time point and cell type.

The various settings of which will obtain different data sets.

• "human-es", human embryonic stem cells.

• "human-embryo", human embryo midbrain.

• "human-ips", human induced pluripotent stem cells.

• "mouse-adult", mouse adult dopaminergic neurons.

• "mouse-embryo", mouse embryo midbrain.

Unfortunately, each of these datasets uses a different set of features. If multiple datasets are to be used simultaneously, users will have to decide how to merge them, e.g., by taking the intersection of common features across all datasets.

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/lamanno-brain.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

La Manno A et al. (2016). Molecular diversity of midbrain development in mouse, human, and stem cells. Cell 167(2), 566-580.

Examples

sce.h.es <- LaMannoBrainData()

sce.h.em <- LaMannoBrainData("human-embryo")

sce.h.ip <- LaMannoBrainData("human-ips")

sce.m.ad <- LaMannoBrainData("mouse-adult")

sce.m.em <- LaMannoBrainData("mouse-embryo")

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