[BioC] DEGraph graph format?

[laurent jacob]

Hi Oliver,

2012/6/9 Oliver Ruebenacker <curoli at gmail.com>:
>     Hello,
>
>  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.

I think Rredland
(http://bioconductor.org/packages/2.4/bioc/html/Rredland.html) parses
biopax in R.

I didn't use it for this package because after that I also needed to
convert the read structure to graphNEL objects, which was not
straightforward. I read the biopax files in Cytoscape, then used
RCytoscape (http://bioconductor.org/packages/release/bioc/html/RCytoscape.html)
to read the networks built by Cytoscape.

Best,

Laurent

-- 
Laurent Jacob
Department of Statistics
UC Berkeley
http://cbio.ensmp.fr/~ljacob