[BioC] extracting interactions between members of the KEGG pathways

[Peter (BioConductor List)]

> Hello,
> 
> I was wondering whether there is an infrastructure in one of the BioC
> packages to extract connections between members of the KEGG pathways. As
> far as I can tell KEGG package allows to get the identifiers of the
> members very easily, however I do not see a way of going one step further
> so to be able to produce a graph (where presence of each edge indicates
> known interaction or same compound )
> 
> Thank you. Any help /suggestion is greatly appreciated.
> 
> Jane

Have you looked at the Rgraphviz package?

"HowTo layout a pathway", focuses on drawing genetic networks using a 
KEGG pathway as an example:

http://www.bioconductor.org/repository/devel/vignette/layingOutPathways.pdf

Installation:
-------------
Install graphviz from www.graphviz.org and then within R simply do:

source("http://www.bioconductor.org/biocLite.R")
biocLite("Ruuid")
biocLite("graph")
biocLite("Rgraphviz")

General Documentation:
----------------------
HowTo Render A Graph Using Rgraphviz:

http://www.bioconductor.org/repository/devel/vignette/Rgraphviz.pdf

Peter