Nothing
PredictMATCH <-function(iicc){
write.fasta <- get("write.fasta",pos="package:seqinr")
read.fasta <- get("read.fasta",pos="package:seqinr")
Prob<-iicc$background
Sequence <- iicc$DNA[[1]]
ncolTFBS<-iicc$model$parametersModel$ncolTFBS
Background<-matrix(,length(Sequence)-ncolTFBS+1,ncolTFBS)
for(X in 1:(length(Sequence)-ncolTFBS+1)){
Background[X,]<-Sequence[X:(X+ncolTFBS-1)]
}
CoreCut<-iicc$model$parametersModel$Corecut/100
threshold<-iicc$threshold
iicc$minim<-iicc$model$parametersModel$minim
iicc$maxim<-iicc$model$parametersModel$maxim
iicc$logodds<-iicc$model$parametersModel$logodds
iicc$minimCore<-iicc$model$parametersModel$minim_core
iicc$maximCore<-iicc$model$parametersModel$maxim_core
iicc$core<-iicc$model$parametersModel$core
iicc$index<-iicc$model$parametersModel$posCore
CoreSeq<- Background[,iicc$index:(iicc$index+4)]
Scores<-apply (Background,1, CalculScores,logodds=iicc$logodds)
CoreScores<-apply(CoreSeq,1,CalculScores, logodds=iicc$core)
Similarity<-sapply(Scores,CalculSimilarity, minim=iicc$minim, maxim=iicc$maxim)
CoreSimilarity<-sapply(CoreScores,CalculSimilarity, minim=iicc$minimCore, maxim=iicc$maximCore)
Scores<-cbind(Similarity, CoreSimilarity, deparse.level=0)
DetectedFactors<-cbind(which(Scores[,1]>=threshold),Scores[Scores[,1]>=threshold,])
DetectedFactors<-DetectedFactors[DetectedFactors[,2]>=CoreCut,]
if(nrow(DetectedFactors)==0){
output<-"No Binding Sites Found"
}else{
output<-lapply(c(1:nrow(DetectedFactors)),function(x){cbind(Sequence=paste(Sequence[DetectedFactors[x,1]:(DetectedFactors[x,1]+iicc$lenmotif)],sep="",collapse=""),pvalue=DetectedFactors[x,2], position=DetectedFactors[x,1])})
}
}
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