Dear Dr. Zhang,
I am starting to use your package KEGGgraph and I've got to a point where I cannot get the information I'd like to get. I've checked the KEGGgraph manual, but I was not able to find a description for that. I am pasting bellow a very small and simple example of what I mean, to try to explain it better.
The example is done with the Human Kegg pathway RAP1 signaling pathway (http://www.kegg.jp/kegg-bin/show_pathway?mmu04015+12801).
The graphical image of this patway in KEGG shows a node (GPCR receptor) where if you drop over the mouse pointer, you are able to see that there are two related entries, 12801-Cnr1 and 13489-Drd2. What I am able to get with KEGGgraph are the entry IDs 12801 and 13489, but what I would like to get are the associated gene names (Cnr1 and Drd2).
I did the following:
tmp <- tempfile()
retrieveKGML(pathwayid='mmu04015' , organism='mmu' , destfile=tmp, method="wget")
pathway <- parseKGML(tmp)
nodes[]@name[] ---> retrieves mmu:12801
nodes[]@name[] ---> retrieves mmu:13489
So, is there a way to jump from this numerical id names to the corresponding Cnr1 and Drd2 gene names?
Thanks very much in advance.