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Materials for tutorial at ajacs68 (Japanese)

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CCCExplorer errors

Rongfang-Shen opened this issue · comments

Hi yuifu,
When I was running CCCExplorer on R using CCCExplorer.R scripts, I meet some problems.
First,I can't find object kegg
then I use: kegg<-pathways("hsapiens", "kegg") ,and Find_KEGG_edge function was rewritten like these

Find_KEGG_edge=function(x){
  x<-x[,c(2,4:6)]
  x=as.matrix(x)
  temp1=x[x[,1]%in%all_symbol&x[,2]%in%all_symbol,]
  if(is.matrix(temp1)){
    temp1[,1]=unlist(as.list(org.Hs.egSYMBOL[temp1[,1]]))
    temp1[,2]=unlist(as.list(org.Hs.egSYMBOL[temp1[,2]]))
  }
  return(temp1)
}

and it all run perfect.
Second, when I run the #simplify network by connecting receptors to TFs directly#partt
length(f) was 0, so there was an error.
I was wondering if I was wrong with the kegg object.
Please help on this.
Many thanks!