matchBindingFactor.BSgenome: Find matches for a binding factor on a layer set containing a...

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

Find matches for a binding factor on a layer set containing a BSgenome sequence

Description

Generate a list of matches for a binding factor against a layerSet object containing a BSgenome sequence. For this (.BSgenome) form, the "Hits" object returned will be a "GRanges" object

Usage

matchBindingFactor.BSgenome(
  layerSet,
  bindingFactor,
  match.layers = names(bindingFactor$profile),
  clusterGap = 10,
  max.window = 1e+07,
  cache.layers = NULL,
  verbose = FALSE
)

Arguments

layerSet	the "layerSet" target
bindingFactor	the "bindingFactor" to match
match.layers	restrict matches to only these named layers (default: all layers in names(bindingFactor$profile))
clusterGap	=10 NOT IMPLEMENTED
max.window	=10000000 on less powerful computers, break up the search into windows of this size.
cache.layers	NULL which named layers to cache hits on (default NULL). Only use for fixed matches (e.g. to genome sequence "LAYER.0")
verbose	output more information to the screen

Value

"GRanges"

See Also

runLayerBinding runLayerBinding.BSgenome modifyLayerByBindingFactor.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_consensus("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))

listOfHits <- matchBindingFactor.BSgenome(layerSet=scLayerSet, bindingFactor=testFactor3)

davetgerrard/GenomicLayers documentation built on Sept. 23, 2024, 3:53 p.m.