distDens: Computing densities for nucleosome positioning simulation
In ChIPsim: Simulation of ChIP-seq experiments

Description Usage Arguments Value Author(s) See Also

These functions compute nucleosome densities for a given parameter set (usually provided through one of the feature classes).

distDens(x, minDist = 175, varDist = 337.5, meanDist = 200)
fragDens(x, minLength, maxLength, meanLength, bind)
indNuc(meanDist = 200, length = 2000, weight = 1)
noNuc(length, weight = 1)
stableDens(x, shift = 10, ratio = 1, weight = 1, stability = 1)
phaseNuc(stable, dist, minDist = 175, length = 2000, meanDist = 200, 
	varDist = (meanDist - minDist) + (meanDist - minDist)^2/2, 
	shift = 10, ratio = 1, weight = 1, stability = 1)
bindLocDens(x, fragLength)

`x`	Position at which the density should be evaluated.
`minDist`	Minimum distance between nucleosomes.
`varDist`	Variance of nucleosome distances.
`meanDist`	Mean distance of nucleosomes.
`minLength`	Minimum fragment length.
`maxLength`	Maximum fragment length.
`meanLength`	Mean fragment length.
`bind`	Position of binding site within fragment.
`length`	Length of region.
`weight`	Weight of feature.
`stable`	Density function for stable nucleosome.
`dist`	Density function of distances between nucleosomes.
`shift`	Distance between alternative position for stable nucleosome.
`ratio`	Ratio of probability mass associated with central and alternative positions for stable nucleosome.
`stability`	Stability of stable nucleosome.
`fragLength`	Length of DNA fragment. If `x` is not in [0, 1] this is used to normalize `x`.