Dear all,
I'm having some problems getting my recursive function to work. At first I
though that maybe my data was too big and I increase option(expressions=50000).
Then I thought that I would try it on some smaller data. Still not working. :(
I would have thought there should be a function for this already, so any
suggestions are welcomed for other methods. I did try igraph but couldn't get
cliques() to give anything useful. Also a quick play with hclust and cut, again
nothing too useful.
Basically the function is trying to find uniquely connected subgraphs. So the
sub-network is only connected by itself and not to other nodes. If everything
is connected then the list (connectedList) should be length of 1 and have every
index in the 1st slot.
cheers,
Paul
findconnection<-function(mat, cutoff){
toList<-function(mat, connectList, cutoff, i, idx){
idx<-which(mat[,idx] < cutoff)
if(length(idx) >= 1){
connectList[[i]]<-idx
for(z in 1:length(idx)){
connectList<-toList(mat, connectList, cutoff,
i, idx[z])
}
}else{
return(connectList)
}
}
connectList<-list()
for(i in 1:ncol(mat)){
connectList<-toList(mat, connectList, cutoff, i, i)
}
return(unique(connectList))
}
foomat<-matrix(sample(c(1,0.5,0), 100, replace=T), nrow=10) ## example data
> foomat
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 0.0 0.5 0.0 0.5 0.5 0.0 0.5 1.0 0.5 0.0
[2,] 0.0 1.0 1.0 0.0 0.0 1.0 0.0 1.0 0.5 1.0
[3,] 1.0 1.0 1.0 1.0 0.5 0.0 0.5 0.5 0.5 0.5
[4,] 0.0 0.5 0.0 0.0 0.5 0.5 0.5 0.0 1.0 0.0
[5,] 0.5 0.5 1.0 1.0 0.5 1.0 1.0 0.5 0.5 0.5
[6,] 0.0 0.5 0.0 0.5 0.5 0.5 0.5 0.5 1.0 1.0
[7,] 1.0 1.0 0.0 1.0 0.0 0.5 1.0 1.0 0.5 0.5
[8,] 0.5 1.0 0.0 0.5 1.0 0.0 1.0 0.0 0.0 0.0
[9,] 0.0 0.5 0.0 0.0 0.5 0.0 0.5 0.0 0.5 0.5
[10,] 1.0 1.0 0.5 1.0 0.0 1.0 0.0 0.0 0.0 0.5
> pb<-findconnection(foomat, 0.01)
Error: C stack usage is too close to the limit
Error during wrapup:
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