R/CalculateHUM_seq.R

In HUM: Compute HUM Value and Visualize ROC Curves

CalculateHUM_seq<-function(data,indexF,indexClass,indexLabel)
{
  indexL=NULL
 
  label=unique(data[,indexClass])
  for(i in 1:length(indexLabel))
  {
  indexL=c(indexL,which(label==indexLabel[i]))
  }
  
  
  output=NULL
  seqMax=NULL

  indexEach=NULL
    
  for(i in 1:length(label))
  {
      vrem=which(data[,indexClass]==label[i])
      indexEach=c(indexEach,list(vrem))
  }
  
  
  len=length(indexL)
  seq=permutations(len,len,1:len)
  
  for(i in 1:length(indexF))
  {
    s_data=NULL
    dataV=data[,indexF[i]]	
    prodValue=1
    for (j in 1:length(indexLabel))
    {
    vrem=sort(dataV[indexEach[[indexL[j]]]])
    
    s_data=c(s_data,list(vrem))
    prodValue = prodValue*length(vrem)
    }
    #seq=sort(d_median,index.return=TRUE)
    
    #out=CalcGene(s_data,seq$ix, prodValue)
    out=CalcGene(s_data,seq,prodValue)
    
    output=c(output,out$HUM)
    seqMax=cbind(seqMax,out$seq)
  }
  
  names(output)=names(data[,indexF,drop = FALSE])
  colnames(seqMax)=names(output)
  
  #return(output)
  return(list(HUM=output,seq=seqMax))
}