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

View source: R/matchBindingFactor.BSgenome.R

matchBindingFactor.BSgenomeR Documentation

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 is likely to 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

"Hits"

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 Feb. 2, 2024, 1:18 p.m.