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Cached database

Source: R/BiocFileCache_database_class.R
BiocFileCache_database.Rd

A cached resource using BiocFileCache.

Usage

BiocFileCache_database(
  source,
  bfc_path = NULL,
  resource_name,
  bfc_fun = .cache_as_is,
  import_fun = read.csv,
  offline = FALSE,
  ...
)

Arguments

source

(ANY) The source of annotation data.

bfc_path

(character, NULL) BiocFileCache is used to cache the database locally and prevent unnecessary downloads. If a path is provided then BiocFileCache will use this location. If NULL it will use the default location (see BiocFileCache::BiocFileCache() for details). The default is NULL.

resource_name

(character) The name given to this resource in the cache. (see BiocFileCache::BiocFileCache() for details).

bfc_fun

(function) A function to process the object before storing it in the cache, e.g. to store an unzipped file in the cache instead of the zipped version. This would prevent needing to unzip the resource each time it is retrieved from the cache, but would mean using more space on disk. The default function does nothing to the resource. See BiocFileCache::bfcdownload() for details.

import_fun

(function) A function to process the object after retrieving it from the cache e.g. it might need to be unzipped before importingas a data.frame. This function should take the path to the cached object as the first input and return a data.frame.

offline

(logical) If offline = FALSE then checks to determine if the resource has expired will be skipped, and retrieved directly from the cache. The default is FALSE.

...

Additional slots and values passed to struct_class.

Value

A BiocFileCache_database object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

  • BiocFileCache

Inheritance

A BiocFileCache_database object inherits the following struct classes:

[BiocFileCache_database] -> [annotation_database] -> [annotation_source] -> [struct_class]

References

Shepherd L, Morgan M (2024). BiocFileCache: Manage Files Across Sessions. R package version 2.10.2.

See also

Other database: sqlite_database

Examples

M = BiocFileCache_database( bfc_path = NULL, resource_name = "bfc",
bfc_fun = function(){}, import_fun = function(){}, offline = FALSE,
tag = character(0), data = data.frame(id=NA), source = "ANY")