mappable_cache: Internal helper functions to manage mappable GRanges in...

In coregenomics/kmap: Generate mappable regions of the genome for a given K-mer length

Description

Reference name for mappable genome of a given k-mer size.

Initialize BiocFileCache assuming NULL to be default.

Path to cached GRanges.

Save GRanges to cache.

Load GRanges from cache.

Usage

mappable_cache_name(bsgenome, kmer = 36)

mappable_cache_bfc(cache_path = NULL)

mappable_cache_path(name, cache_path = NULL)

mappable_cache_save(granges, name, cache_path = NULL, force = FALSE)

mappable_cache_load(name, bsgenome, cache_path = NULL)

Arguments

bsgenome	Apply the sequence information from this BSgenome or BSgenomeViews object to loaded GRanges.
kmer	The exact size of DNA segments to check for unique mapping in the genome.
cache_path	Path to initialize BiocFileCache object at a non-default path storage location.
name	Reference name generated by mappable_cache_name to access BiocFileCache.
granges	GRanges to save to cache.
force	Save to cache even if an object already exists. Only used to simulate a name collision for unit tests and not intended for use otherwise; using this will break your ability to run mappable_cache_load!

Value

mappable_cache_name returns a character vector reference name for a given bsgenome and kmer size.

mappable_cache_bfc returns a BiocFileCache object.

mappable_cache_path returns a character vector of the path to the cached file path if the file exists, otherwise NULL.

mappable_cache_save returns the path to the saved cache file.

mappable_cache_load returns the GRanges of mappable areas of the genome from the cache.

coregenomics/kmap documentation built on June 4, 2019, 4:11 p.m.