generateHitsCache: Generate a cache of binding factor within a LayerList

In davetgerrard/GenomicLayers: Simple, sequence-based simulation of epi-genomes.

Generate a cache of binding factor within a LayerList

Description

Generate and attach a cache of binding factor hit positions for named binding factors on certain levels. This is an internal function called from runLayerBinding.BSgenome In turn it uses matchBindingFactor.BSgenome to generate hits.

Usage

generateHitsCache(layerList, factorSet, cache.layers = NULL, verbose = FALSE)

Arguments

layerList	a "Layerlist" object containing a layerSet based on a BSgenome and other meta-data
factorSet	a "list" of "bindingFactor" objects
cache.layers	which named layers to cache hits on (default NULL)
verbose	give more output

Value

"LayerList"

See Also

runLayerBinding.BSgenome matchBindingFactor.BSgenome

Examples

require(Biostrings)
require(BSgenome.Scerevisiae.UCSC.sacCer3)

genome <- BSgenome.Scerevisiae.UCSC.sacCer3   # for convenience


scLayerSet <- createLayerSet.BSgenome(genome=genome, n.layers = 5, verbose=TRUE)

testFactor3 <- createBindingFactor.DNA_motif("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.1", "LAYER.3"), profile.marks = c(0,0), 
                                             mod.layers = c("LAYER.2", "LAYER.4"), mod.marks=c(0,1))

generateHitsCache(layerList=scLayerSet, factorSet=list(testFactor3))

davetgerrard/GenomicLayers documentation built on Feb. 2, 2024, 1:18 p.m.