CalculRedundancy: CalculRedundancy: To calculate the redundancy

In MEET: MEET: Motif Elements Estimation Toolkit

Description

This function calculates the redundancy (order) of a random variable X with N possible states.

Usage

CalculRedundancy(Factortrans, q,iicc)

Arguments

Factortrans	A set of aligned nucleotide sequences
q	Renyi Order
iicc	A list options

Author(s)

Joan Maynou <[e-mail]>

See Also

redundancy, entropy.Shannon,entropy.Renyi, correction.redundancy, correction.entropy, correctionaprox

Examples

data(TranscriptionFactor)
data(BackgroundOrganism)
data(RenyiOrder)
data(iicc)
Factortrans<-TranscriptionFactor
correction<-correction.entropy(q,p=nrow(Factortrans),long=1,iicc=iicc)
iicc$Herror<-iicc$HXmax<-iicc<-classentropy<-NULL
iicc$Herror<-slot(correction,"Herror")
iicc$classentropy<-"Shannon"
training.set<-TranscriptionFactor
 wind<-probability(training.set,Prob,missing.fun=NULL)
iicc$HXmax<-H<-switch(iicc$classentropy, "Shannon"=entropy.Shannon(wind),"Renyi"=entropy.Renyi(iicc$background,q))
CalculRedundancy(Factortrans,q,iicc)

MEET documentation built on May 2, 2019, 5:52 p.m.