KEGG graph or pathway to Adjacency matrix

Question

[saamar.rajput]

Hello guys,

I am trying to get the adjacency matrix out of the KEGG graph or pathway in R. I did search online but could not find any tools or function that could help me get what i want. I did retrieve the KEGG XML file and did some further retrieving from it but could not get the adjacency matrix.

Anybody who did something like this before? Would really appreciate some help.

Answer 1

[Jean-Karim Heriche]

You could have a look at the PathNet package. However, it should be a relatively easy scripting task: simply set A(i,j)=1 if there is a link between gene i and gene j, 0 otherwise. Note that since the graph is directed, in general, A(i,j) != A(j,i).