runLayerBinding.BSgenome: Run the layer binding simulation on a BSgenome object

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

Run the layer binding simulation on a BSgenome object

Description

Simulate layer binding by the binding factor on the layerList

Usage

runLayerBinding.BSgenome(
  layerList,
  factorSet,
  iterations = 1,
  bf.abundances = rep(10000, length(factorSet)),
  watch.function = function(x) {
 },
  collect.stats = FALSE,
  keep.stats = TRUE,
  target.layer = 2,
  cache.layers = "LAYER.0",
  verbose = FALSE,
  ...
)

Arguments

layerList	a "Layerlist" object containing a layerSet and other meta-data
factorSet	a "list" of "bindingFactor" objects
iterations	deprecated - do not use
bf.abundances	10000 the quantities of each "bindingFactor" in "factorSet"
watch.function	have this function execute during each iteration e.g. print something
collect.stats	FALSE collect a table of stats each iteration
keep.stats	TRUE whether to retain data contained in $history.
target.layer	NOT IMPLEMENTED
cache.layers	store hits for these layers if they are immutable (e.g. LAYER.0 sequence) default= "LAYER.0". Set to NULL to prevent caching
verbose	give more output

Value

"LayerList"

See Also

runLayerBinding matchBindingFactor.BSgenome modifyLayerByBindingFactor.BSgenome generateHitsCache createLayerSet.BSgenome createBindingFactor.DNA_motif

Examples

# test to show whole genome layer binding 
# three factors are created, the third can only hit after the first has modified.

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

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


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

testFactor2 <- createBindingFactor.DNA_consensus("test", patternString="ACTGGGCTA")

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))

# check that a profile looking for 1 will not find any.  N.B this WILL bind AFTER testFactor2
testFactor4 <- createBindingFactor.DNA_consensus("test", patternString="ACTGGGCTA", profile.layers = c("LAYER.3", "LAYER.4"), profile.marks = c(0,1), 
                                             mod.layers = c("LAYER.1", "LAYER.2"), mod.marks=c(0,1))

 
# now can match things genome wide. Need to run layerBinding and modification.

# need to have a factorSet, a list of bindingFactors

testFS <- list(testFactor2=testFactor2, testFactor3=testFactor3, testFactor4=testFactor4)

 
# with the above configuration, there are 41 possible sites across the genome, setting bf.abundances=30, restricts the number that are marked, so the number of potential sites reduces.
modTest <- runLayerBinding.BSgenome(layerList=scLayerSet, factorSet=testFS, verbose=TRUE, bf.abundances=30)

davetgerrard/GenomicLayers documentation built on Nov. 21, 2024, 6:21 a.m.