Nothing
PredictDivergence <-function(iicc){
require("MEET")
require("seqinr")
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
training.set<-Factortrans<-matriu<-iicc$Transcriptionfactor
iicc$D <- iicc$correction_1rOrdre <- iicc$probparella<-NULL
iicc$correction_1rOrdre_m1<-iicc$Mperfil<-iicc$q<- NULL
iicc$HXmax<-iicc$HX<-iicc$q<-NULL
iicc$Divergence<-iicc$interA<-iicc$interB<-iicc$classentropy<-NULL
Prob<-iicc$background
#iicc$missing.fun=TRUE
q<-iicc$q<-iicc$model$parameterModel$Order
if (q==1) {iicc$classentropy<-"Shannon"
}else{
iicc$classentropy<-"Renyi"
}
k<-length(iicc$DNA[[1]])
out<-lapply(seq(1,length(iicc$DNA),1), function(r){vector(mode="numeric",length=(k-ncol(Factortrans)+1))})
out_diff<-lapply(seq(1,length(iicc$DNA),1), function(r){})
iicc$D<-iicc$model$parameterModel$D
iicc$HXmax<-iicc$model$parameterModel$HXmax
iicc$correctioc_1rOrdre<-iicc$model$parameterModel$correction_1rOrdre
iicc$Entropy<-iicc$model$parameterModel$HX
iicc$Mperfil<-iicc$model$parameterModel$Mperfil
iicc$interA<-iicc$model$parameterModel$interA
iicc$interB<-iicc$model$parameterModel$interB
iicc$Divergence<-iicc$model$model
names(iicc$Divergence)<-as.character(c(1:length(iicc$Divergence)))
nameDivergence<-as.character(c(1:length(iicc$Divergence)))
lengthname<-length(nameDivergence)
Results<-NULL
ncoltraining<-ncol(iicc$Transcriptionfactor)
MachineDouble<-.Machine$double.eps
for(i in c(1:length(iicc$DNA))){
index<-results<-resultat<-threshold<-a<-Pvalor<-Index<-NULL
validation.set_x <- iicc$DNA[[i]]
iicc$longDNA<-length(iicc$DNA[[i]])
timein<-proc.time()
out[[i]]<-.Call("loopDIVERGENCE",
validationsetx=validation.set_x,
lengthDNA=k,
ncoltraining=ncoltraining,
lengthname=lengthname,
interA=iicc$interA,
interB=iicc$interB,
nameDivergence=nameDivergence,
MachineDouble=MachineDouble,
Divergence=iicc$Divergence,
D=iicc$D,
Mperfil=iicc$Mperfil)
timeout<-proc.time()
cat("Run time Divergence Detection",timeout[3]-timein[3],"\n")
a<-rev(sort(as.vector(t(out[[i]]))))
out_diff[[i]]<-as.vector(t(out[[i]]))
jj<-1
threshold<-pvalue(a[jj],out_diff[[i]])
while (threshold<iicc$threshold){
index<-as.numeric(which(out_diff[[i]]==a[jj]))
if (length(index)==1){
Pvalor<-cbind(Pvalor,threshold)
Index<-cbind(Index,index)
jj<-jj+1
}else{
for (ii in c(1:length(index))){
Pvalor<-cbind(Pvalor,threshold)
Index<-cbind(Index,index[ii])
}
jj<-jj+length(index)
}
threshold<-pvalue(a[jj],out_diff[[i]]) }
results<-matrix(,length(Index),3,dimnames=list(c(1:length(Index)),c("Position","Value","Direction")))
results[,1]<-as.numeric(Index[1,])
results[,2]<-as.numeric(round(as.numeric(Pvalor[1,]),7))
if (iicc$direction!="b"){
results[,3]<-iicc$direction
}else{
if (i==1) {results[,3]<-"f"
}else{
results[,3]<-"r"
}
}
Sequence<-vector(mode="character", length=length(Index))
for(ii in c(1:length(Index))){
if (results[ii,3]=="f"){j<-1
}else{
j<-2}
sequencia<-t(as.matrix(iicc$DNA[[j]][c(Index[ii]:(Index[ii]+ncol(iicc$Transcriptionfactor)))]))
Sequence[ii]<-paste(sequencia, sep="", collapse="")
}
resultat <- cbind(results, Sequence)
Results<-rbind(Results,resultat)
}
Results
}
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