I have a subnetwork from PPI network. The edges of the subnetwork is undirected.
I would like to convert the undirected edges into directed edges based on pathway information (using the knowledge from KEGG/reactome etc). Ideally, I would like convert the subnetwork into one giant pathway. I can see that one option is do it manually using tool like Pathvisio. But I have ~600 nodes in the subnetwork. So I am interested to know if there is any automated way to convert/merge pathway information with PPI graphs. Any suggestions, methods or info on cytoscape,bioconductor tools will be helpful.