stableFeature: Generating Features
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Arguments Value Author(s) See Also Examples

These functions are used to generate the parameters for different nucleosome positioning related features.

stableFeature(start, minDist = 175, weight = seq(0.1, 1, by = 0.1), 
	shift = c(0, 5, 10), ratio = seq(0, 4, by = 0.25), 
	stability = seq(0.1, 5, by = 0.1), weightProb, shiftProb, 
	ratioProb, stabilityProb, ...)
phasedFeature(minDist = 175, length = seq(1000, 10000, by = minDist), 
	meanDist = minDist:300, lengthProb, meanDistProb, start, ...)
fuzzyFeature(start, length = seq(1000, 10000, by = 1000), 
	meanDist = 175:400, lengthProb, meanDistProb, ...)
nfrFeature(start, length = seq(50, 500, by = 10), 
	weight = seq(0.1, 1, by = 0.1), lengthProb, weightProb, ...)

`start`	Start location of feature on chromosome.
`minDist`	Minimum distance between nucleosomes.
`length`	A numeric vector giving possible values for the length of the feature.
`meanDist`	A numeric vector giving possible values for the mean distance between nucleosomes.
`weight`	A numeric vector giving possible values for the weight of the feature.
`shift`	A numeric vector giving possible values for the distance between favoured positions of stable nucleosomes.
`ratio`	A numeric vector giving possible values for the ratio between probabilities for alternative and central position of stable nucleosomes.
`stability`	A numeric vector giving possible values for the stability of stable nucleosomes.
`lengthProb`	Length distribution of feature. This corresponds to the state duration distribution of the underlying generating model.
`meanDistProb`	Distribution of mean distances between nucleosomes.
`weightProb`	Distribution of feature weights.
`shiftProb`	Distribution of distances between favoured positions of stable nucleosome.
`ratioProb`	Ratio distribution.
`stabilityProb`	Stability distribution.
`...`	Further arguments (currently ignored).