FeatureGenerators {ChIPsim} | R Documentation |
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). |
A list of parameters for the corresponding feature type. These parameters are later used to compute nucleosome densities.
Peter Humburg
feature <- stableFeature(200)