Sorry bad example. My data is undirected. It's a correlation matrix so probably better to look at something like:
foomat<-cor(matrix(rnorm(100), ncol=10))
foomat
mine are pvalues from the correlation but same idea.
On 14 Jul 2011, at 11:23, Erich Neuwirth wrote:
> cliques only works for undirected graphs.
> Your matrix is not symmetric, therefore
> the graph is directed.
>
>
> On 7/14/2011 8:53 AM, Benton, Paul wrote:
>> 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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>>
>