cache: Package cache

In lgatto/rpx: R Interface to the ProteomeXchange Repository

Package cache

Description

Function to access and manage the cache. rxpCache() returns the central rpx cache. pxCachedrojects() prints the names of the cached projects and invisibly returns the cache table.

Usage

rpxCache()

pxCachedProjects(cache = rpxCache(), rpxprefix = "^\\.rpx(2?)")

Arguments

cache	Object of class BiocFileCache.
rpxprefix	character(1) defining the resourne name prefix in cache. Default is "^\\.rpx(2?)" to match objects of class PXDataset and PXDataset2.

Details

The cache is an object of class BiocFileCache, and created with BiocFileCache::BiocFileCache(). It can be either the package-wide cache as defined by rpxCache() or an instaned provided by the user.

When projects are cached, they are given a resource name (rname) composed of the .rpx prefix followed by the ProteomeXchange identifier. For example, project PXD000001 is named .rpxPXD000001 (.rpx2PXD000001 for the PXDataset2 class) to avoid any conflicts with other resources that user-created resources.

Value

The rpxCache() function returns an instance of class BiocFileCache. pxCachedProjects() invisbly returns a tibble of cached ProteomeXchange projects.

Author(s)

Laurent Gatto

Examples

## Default rpx cache
rpxCache()

## Not run: 

## Set up your own cache by providing a file or a directory to
## BiocFileCache::BiocFileCache()
my_cache <- BiocFileCache::BiocFileCache(tempfile())
my_cache
px <- PXDataset("PXD000001", cache = my_cache)
pxget(px, "erwinia_carotovora.fasta", cache = my_cache)


## List of cached projects
pxCachedProjects() ## default rpx cache
pxCachedProjects(my_cache)

## To delete project a project from the default cache, first find
## its resource id (rid) in the cache
px1_cache_info <- pxCacheInfo(px)
(rid <- px1_cache_info["rid"])

## Then remove it with BiocFileCache:: bfcremove()
BiocFileCache:::bfcremove(my_cache, rid)
pxCachedProjects(my_cache)

## End(Not run)

lgatto/rpx documentation built on Oct. 2, 2023, 9:15 p.m.