EBSeq/R/TopCts.R

   1 TopCts <-
   2 function(pvalue, PP=NULL, TrueNames, TopNum){
   3         NumOfMethods=ncol(pvalue)
   4         puse=pvalue
   5         if(1%in%PP)puse[,PP==1]=1-pvalue[,PP==1]
   6         #puse.list=data.frame(puse)
   7         FD=matrix(rep(0,NumOfMethods*TopNum),ncol=NumOfMethods)
   8 #       Rank=apply(puse,2,rank)
   9 #       for(i in 1:TopNum)
  10 #               FD[i,]=sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]%in%TrueNames))
  11 #       FD=sapply(1:TopNum, function(i)sapply(1:NumOfMethods, function(j)sum(!rownames(Rank)[Rank[,j]<=i]%in%TrueNames)))
  12         for (s in 1:NumOfMethods){
  13                 tmp=puse[,s]
  14                 names(tmp)=rownames(puse)
  15                 sorttmp=sort(tmp)
  16                 for( c in 2:TopNum)
  17                         FD[c, s]=FD[(c-1),s]+as.numeric(!names(sorttmp)[c]%in%TrueNames)
  18         }
  19         FD
  20         #matplot(TopNum,FD,type="l",ylim=c(0,1),xlab="Top DE selected", ylab="FDR")
  21         #legend("rightbottom",col=1:TopNum, lty=1:TopNum, names)
  22         }
  23