mappable: Return mappable regions of a genome for a given k-mer size.

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

Description

Genomes contain repetitive DNA, causing even long segments of DNA to map in multiple places. For a fixed segment size kmer, link{mappable} checks whether DNA can map in multiple places in the genome and returns only regions which uniquely map.

Usage

mappable(genome, kmer = 36, BPPARAM = bpparam(), verbose = TRUE,
  cache_path = NULL)

Arguments

genome	Single character vector genome identifier. Short hand identifiers like "hg38" can be used in interactive sessions but can fail in scripts due to intended behavior of getBSgenome preferring unambiguous full identifiers like "BSgenome.Hsapiens.UCSC.hg38".
kmer	The exact size of DNA segments to check for unique mapping in the genome.
BPPARAM	An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to BiocParallel functions.
verbose	Print messages of the calculation steps and their elapsed time. Unfortunately, during first-time calculation, messages from qAlign are always shown because qAlign runs as a subprocess.
cache_path	Path to initialize BiocFileCache object at a non-default path storage location.

Value

The GRanges-class of mappable DNA sequences.

Examples

## Not run: 
mappable("BSgenome.Scerevisiae.UCSC.sacCer2")

## End(Not run)
 

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