MEET (version 5.1.1)

PredictDivergence: A set of functions for detection of Transcription Factor Binding Sites by means of Divergence

Description

PredictDivergence contains a set of functions for detection of Transcription Factor Binding sites through parametric divergence. This algorithm evaluates the variation on the total Renyi entropy of a set of sequences assuming correlation between positions in the bindng sequence.

Usage

PredictDivergence(iicc)

Arguments

iicc

A set of inicial conditions for the MEET-package (mode, method, background, alignment, threshold, parameters, Transcriptionfactor, nummotif, lenmotif, sentit, position, missing, vector, gapopen, maxiters, gapextend)

Details

This function integrates the Mutual Information (Renyi order equal 1) and parametric divergence (Renyi order different 1)

References

J. Maynou, M. Vallverdu, F. Claria, J.J. Gallardo-Chacon, P. Caminal and A. Perera," Transcription Factor Binding Site Detection through Position Cross-Mutual Information variability analysis". 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

See Also

PredictEntropy, PredictMEME, PredictMDscan, PredictPCA and PredictMATCH

Examples

require("MEET")
data(HomoDivergence)
iicc[["AP1"]]$threshold<-0.01
PredictDivergence(iicc[["AP1"]])