Hi Anupam,

  I am the author and the maintainer of the KEGGgraph, and I will try to
answer your questions.

  Although I have never done this before, but I believe the following
pipeline should do the job

  (1) Download the pathway KGML files with retrieveKMGL function or manually
from the KEGG FTP server
  (2) Parse them in a list with parseKGML2Graph
  (3) use lapply(list, nodes) to list the nodes of each graph
  (4) Build a NxN matrix, with N equalling to the number of the KGML files.
Fill the matrix with the intersecting nodes between each pathway.
  (5) Convert the matrix into a (undirected) graph

  Best wishes,
David


2009/11/27 anupam sinha <anupam.contact@gmail.com>

> Dear all,
>                 I am using the KEGGgraph package to construct metabolic
> networks of various organisms and study their topological properties.My
> query though is : Can the package KEGGgraph be used to construct a
>  weighted
> directed graph in which the nodes are the pathways themselves and they are
> connected if they share enzymes ? The no. of enzymes any two pathways share
> can be used to give a  weight to the edge between the two pathways (nodes
> in
> this case). Thanks in advance for any help.
>
>
>
> Regards,
>
> Anupam
>
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-- 
Jitao David Zhang
Biological Statistics and Computational Biology Ph.D.
Division of Molecular Genome Analysis
DKFZ, Heidelberg D-69120, Germany

http://www.NextBioMotif.com/

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