Nothing
PredictPCA <-function(iicc){
require("pcaMethods")
Prob<-iicc$background
ncolTFBS<-iicc$model$parametersModel$ncolTFBS
nPcs<-iicc$parametersIdeal
threshold<-iicc$threshold
Sequence <- iicc$DNA[[1]]
missing<-iicc$missing
NumericalMatrix<-iicc$model$parametersModel$NumericalMatrix
model<-iicc$model$model
parametersQ<-iicc$model$parametersModel$JacksonPars
DNA<-sapply(X=c(1:(length(Sequence)-ncolTFBS+1)), FUN=function(X, ncolTFBS){Sequence[X:(X+ncolTFBS-1)]}, ncolTFBS=ncolTFBS)
DNA<-t(DNA)
DNAnum<-apply(DNA,1,function(x){as.vector(t(NumericalMatrix[x,]))})
DNAnum<-t(DNAnum)
matrix.residuals<-residuals.pcaRes(model,DNAnum, nPcs=model@nPcs)
residus<-apply(matrix.residuals,1,function(vector){vector%*%vector})
Score<-sapply(residus,QtoJackson, h0=parametersQ$h0, x1=parametersQ$x1,x2=parametersQ$x2,x3=parametersQ$x3 )
DetectedFactors<-cbind(which((1-Score)<=threshold),Score[(1-Score)<=threshold])
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]+ncolTFBS)],sep="",collapse=""),pvalue=1-DetectedFactors[x,2], position=DetectedFactors[x,1], direction=iicc$direction)})
}
return(output)
}
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