defaultGenerator: Defaults for Feature Generator

In ChIPsim: Simulation of ChIP-seq experiments

Description

Functions to generate defaults for makeFeatures.

Usage

defaultGenerator()
defaultTransition()
defaultInit(prob=c(0.2, 0.05, 0, 0.25, 0.5), 
	states=c("ReversePhasedFeature", "StableFeature", 
		"PhasedFeature", "NFRFeature", "FuzzyFeature"))
defaultLastFeat(isEnd = c(FALSE, rep(TRUE, 4)), 
	states = c("ReversePhasedFeature", "StableFeature", 
		"PhasedFeature", "NFRFeature", "FuzzyFeature"))

Arguments

prob	Numeric vector giving the initial state distribution. This will be normalised if the probabilities do not add up to 1.
isEnd	Logical vector indicating which states, i.e. features, are allowed to be last in the sequence.
states	Character vector of state names.

Details

These functions generate data structures that can be passed as arguments to makeFeatures. Using this set of functions will create a nucleosome positioning simulation. Some of the defaults can be modified by passing different values to defaultInit and defaultLastFeat.

Value

Return values are suitable as arguments generator, transition, init and lastFeat of makeFeatures. See the documentation of makeFeatures for more detail.

Author(s)

Peter Humburg

Examples

	set.seed(1)
	## generate defaults
	generator <- defaultGenerator()
	transition <- defaultTransition()
	lastFeat <- defaultLastFeat()
	
	## change the initial state distribution such that it 
	## always starts with a fuzzy feature
	init <- defaultInit(c(0, 0, 0, 0, 1))
	
	## now generate some features for a stretch of 1 million base pairs 
	features <- makeFeatures(generator=generator, transition=transition, 
		lastFeat=lastFeat, init=init, length=1e6)

ChIPsim documentation built on Nov. 8, 2020, 8:09 p.m.