MEET (version 5.1.1)

divergence.Renyi: Renyi divergence

Description

This function calculates parametric divergence (Renyi Order different 1)

Usage

divergence.Renyi(training.set, pmX, pmXY, q, correction)

Arguments

training.set

A set of aligned nucleotide sequences

pmX

Relative frequency of a nucleotide at a motif position (position independency model) as an estimation of the probability of this fact.

pmXY

To extend to pmX to include of correlated positions (position dependency model)

q

Renyi Order

correction

Correction of the Finite Sample Size Effect

See Also

divergence.Shannon, PredictDivergence

Examples

require("MEET")
data(iicc)
data(BackgroundOrganism)
training.set<-iicc$Transcriptionfactor
q<-iicc$q<-0.5
correction<-correction.entropy(q,p=nrow(training.set),long=1,iicc)
HXmax<-iicc$HXmax
pmX<-probability(training.set,Prob)
Probtrans<-probability.couple(Prob)
H<-entropy.Renyi(pmX,q)
pmXY<-joint.probability(training.set, Prob, Probtrans)
HXY<-entropy.joint(pmXY,q,iicc)
divergence.Renyi(training.set,pmX,pmXY,q,correction)