manifest: HCA File Querying

In Bioconductor/hca: Exploring the Human Cell Atlas Data Coordinating Platform

HCA File Querying

Description

manifest() takes a list of user provided project titles to be used to query the HCA API for information about available manifest files.

manifest_cache() is the default location of the cache of downloaded manifest.

Usage

manifest(filters = NULL, catalog = NULL, update_cache = FALSE)

manifest_cache(create = FALSE)

Arguments

filters	hca filter object
catalog	character() name of catalog
update_cache	logical(1) when TRUE, update an existing cached resource by querying the HCA data server.
create	logical(1) create the default cache location, if it does not yet exist.

Details

manifest_cache() can be useful when it is necessary to 'clean up' the cache, e.g., BiocFileCache::cleanbfc() or more dramatically unlink(manifest_cache(), recursive = TRUE).

Value

manifest_cache() returns the path to the default cache. Use this as the ⁠cache=⁠ argument to BiocFileCache().

Examples

manifest_filter <- hca::filters(
    projectId = list(is = "4a95101c-9ffc-4f30-a809-f04518a23803"),
    fileFormat = list(is = "loom"),
    workflow = list(is = c("optimus_v4.2.2", "optimus_v4.2.3"))
)
## Not run: 
result <- manifest(manifest_filter)
result

## End(Not run)
manifest_cache(create = FALSE)

Bioconductor/hca documentation built on March 27, 2024, 3:15 a.m.