searchReferences: Search reference metadata

In LTLA/celldex: Index of Reference Cell Type Datasets

Search reference metadata

Description

Search for reference datasets of interest based on matching text in the associated metadata.

Usage

searchReferences(
  query,
  cache = cacheDirectory(),
  overwrite = FALSE,
  latest = TRUE
)

Arguments

query	String or a gypsum.search.object, see Examples.
cache, overwrite	Arguments to pass to fetchMetadataDatabase.
latest	Whether to only consider the latest version of each dataset.

Details

The returned DataFrame contains the usual suspects like the title and description for each dataset, the number of rows and columns, the organisms and genome builds involved, whether the dataset has any pre-computed reduced dimensions, and so on. More details can be found in the Bioconductor metadata schema at https://github.com/ArtifactDB/bioconductor-metadata-index.

Value

A DataFrame where each row corresponds to a dataset, containing various columns of metadata. Some columns may be lists to capture 1:many mappings.

Author(s)

Aaron Lun

See Also

surveyReferences, to easily obtain a listing of all available datasets.

Examples

searchReferences(defineTextQuery("immun%", partial=TRUE))[,c("name", "title")]
searchReferences(defineTextQuery("10090", field="taxonomy_id"))[,c("name", "title")]
searchReferences(
   defineTextQuery("10090", field="taxonomy_id") &
   defineTextQuery("immun%", partial=TRUE)
)[,c("name", "title")]

LTLA/celldex documentation built on June 3, 2024, 4:53 p.m.