> 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/layingOutPathway s.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

Another issue is availability of cMAP data: data for download is very different from that driving cMAP online querries. The downloadable data is only a small subset of online data, and there are quite some discrepencies between the two. The downloadable data is unchanged since early 2005. Li > There is some stuff done in the cMAP and pathRender packages, but this > has not progressed that far, mostly due to a lack of resources > > cMAP is a meta-data package which has information from both KEGG and > BioCarta (original data from the NCI) > > pathRender is in the development archive > > best wishes > Robert > > > Jane Fridlyand wrote: >> 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 >> >> >> >> >> >> ******************************************************************* ************* >> Jane Fridlyand, Assistant Professor >> Department of Epidemiology and Biostatistics >> Center for Bioinformatics and Molecular Biostatistics >> UCSF Comprehensive Cancer Center, >> Box 0128 San Francisco, CA 94143-0128 >> Office: Room N224 Tel: (415)476-0168 Fax: (415)502-3179 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >