[BioC] DEGraph graph format?

[Oliver Ruebenacker]

     Hello,

On Fri, Jun 8, 2012 at 4:30 PM, laurent jacob <laurent.jacob at gmail.com> wrote:
> Hi Hamid,
>
> 2012/6/7 Hamid Bolouri <hbolouri at fhcrc.org>:
>
>>>library(NCIgraphData)
>>>data("NCI-cyList")
>>> NCI.cyList[[1]]
>> A graphNEL graph with directed edges
>> Number of Nodes = 35
>> Number of Edges = 40
>
> The graphs NCI-cyList cannot directly be used with DEGraph: they are
> raw representations of the NCI biopax files. In particular, the nodes
> of the graph do not correspond to genes:

  Does this package use a BioPAX parser that could be used for other
BioPAX data? Does it read level 2 or level 3 or both?

  I'm looking for a BioPAX parser and would be willing to help build
one if none exists.

  Thanks!

     Take care
     Oliver

-- 
Oliver Ruebenacker
Bioinformatics Consultant (http://www.knowomics.com/wiki/Oliver_Ruebenacker)
Knowomics, The Bioinformatics Network (http://www.knowomics.com)
SBPAX: Turning Bio Knowledge into Math Models (http://www.sbpax.org)