distDens {ChIPsim} | R Documentation |
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 |
Density evaluated at the given position.
Peter Humburg