Hmemory: Library of entropy values

In MEET: MEET: Motif Elements Estimation Toolkit

Description

This function calculates entropy values from all combinations possibles of nucleotides given a matrix of TFBS sequences.

Usage

Hmemory(iicc, training.set)

Arguments

iicc	A set of inicial conditions for the MEET-package
training.set	A set of nucleotide sequences

Author(s)

Joan Maynou <[e-mail]>

See Also

Hread

Examples

library(seqinr)
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
data(iicc)
pathMEET<-system.file("exdata",package="MEET") 	
i<-1
factor<-switch(iicc$alignment, "CLUSTALW"=align.clustalw(filein=paste(pathMEET,"AP1.fa",sep="/"), fileout="Sq.fa", call=iicc$call.clustalw), "MUSCLE"=align.muscle(filein="setTF.fa", fileout="Sq.fa", gapopen=iicc$gapopen, maxiters=iicc$maxiters, gapextend=iicc$gapextend, call=iicc$call.muscle),"MEME"=align.MEME(filein="setTF.fa",fileout="Sq.fa",iicc),"NONE"=Read.aligned("setTF.fa"), stop("Alignment method not included"))		
q<-iicc$q<-iicc$correction_1rOrdre<-iicc$Herror<-iicc$HXmax<-iicc$Redundancia_corregida<-iicc$ErrorHX<-iicc$classentropy<-iicc$Entropy<-NULL
q<-iicc$q<-iicc$vector[i]					  
if (q==1) {iicc$classentropy<-"Shannon"
		}else{
		iicc$classentropy<-"Renyi"  
	  }
   iicc$correction_1rOrdre <- correction.entropy(q,nrow(factor),1,iicc)
   iicc$Herror<-slot(iicc$correction_1rOrdre,"Herror")
   iicc$HXmax<-	 iicc$Herror[nrow(factor)]
   iicc$Redundancia_corregida<-CalculRedundancy(factor,q,iicc)
   iicc$ErrorHX<-slot(iicc$correction_1rOrdre,"sderror")[nrow(factor)]
   Results<-Hmemory(iicc,factor)

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