fetchDataset: Fetch a dataset from the gypsum backend

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

Fetch a dataset from the gypsum backend

Description

Fetch a dataset (or its metadata) from the gypsum backend.

Usage

fetchDataset(
  name,
  version,
  path = NA,
  package = "scRNAseq",
  cache = cacheDirectory(),
  overwrite = FALSE,
  realize.assays = FALSE,
  realize.reduced.dims = TRUE,
  ...
)

fetchMetadata(
  name,
  version,
  path = NA,
  package = "scRNAseq",
  cache = cacheDirectory(),
  overwrite = FALSE
)

Arguments

name	String containing the name of the dataset.
version	String containing the version of the dataset.
path	String containing the path to a subdataset, if name contains multiple datasets. Defaults to NA if no subdatasets are present.
package	String containing the name of the package.
cache, overwrite	Arguments to pass to saveVersion or saveFile.
realize.assays, realize.reduced.dims	Logical scalars indicating whether to realize assays and reduced dimensions into memory. Dense and sparse ReloadedArray objects are converted into ordinary arrays and dgCMatrix objects, respectively.
...	Further arguments to pass to readObject.

Value

fetchDataset returns the dataset as a SummarizedExperiment or one of its subclasses.

fetchMetadata returns a named list of metadata for the specified dataset.

Author(s)

Aaron Lun

See Also

https://github.com/ArtifactDB/bioconductor-metadata-index, on the expected schema for the metadata.

saveDataset and uploadDirectory, to save and upload a dataset.

surveyDatasets and listVersions, to get possible values for name and version.

Examples

fetchDataset("zeisel-brain-2015", "2023-12-14")
fetchMetadata("zeisel-brain-2015", "2023-12-14")

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