fetchReference: Fetch a reference dataset

In LTLA/CellTypeReferences: Index of Reference Cell Type Datasets

Fetch a reference dataset

Description

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

Usage

fetchReference(
  name,
  version,
  path = NA,
  package = "celldex",
  cache = cacheDirectory(),
  overwrite = FALSE,
  realize.assays = FALSE,
  ...
)

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

Arguments

name	String containing the name of the reference dataset.
version	String containing the version of the dataset.
path	String containing the path to a subdataset, if name contains multiple reference 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	Logical scalar indicating whether to realize assays into memory. Dense and sparse ReloadedArray objects are converted into ordinary arrays and dgCMatrix objects, respectively.
...	Further arguments to pass to readObject.

Value

fetchReference returns the dataset as a SummarizedExperiment. This is guaranteed to have a "logcounts" assay with log-normalized expression values, along with at least one character vector of labels in the column data.

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.

saveReference and uploadDirectory, to save and upload a dataset.

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

Examples

fetchReference("immgen", "2024-02-26")
str(fetchMetadata("immgen", "2024-02-26"))

LTLA/CellTypeReferences documentation built on June 1, 2024, 12:12 p.m.