CCCExplorer errors
Rongfang-Shen opened this issue · comments
RongfangShen commented
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!