Hello all,

I've been trying to create the most complete possible compound map for
an organism, and KEGGgraph was the best approach until now.

Someone already worked with graphs metabolites in R?

I have a doubt if the KEGGgraph merging process can miss nodes, that's
because,
looking at the compounds in each reaction:

    read.delim(paste("http://rest.kegg.jp/link/reaction/", orgId,
sep=""),header=FALSE)
    read.delim(paste("http://rest.kegg.jp/link/compound/", orgId,
sep=""),header=FALSE)

 where orgId is the tree letter organism code, I have a set of compounds
different than the one retrivied bellow:

When I use the mergeGraphs function:


for (i in 1:length(allPath)) {
        retrieveKGML(allPath[i], organism=orgId, destfile=tmp,
method="wget", quiet=TRUE)
        lg[[i]]  <- parseKGML(tmp)
        if(length(lg[[i]]@reactions))  lt[[i]] <-
KEGGpathway2reactionGraph(lg[[i]])
    }
    lt <- lt[!unlist(lapply(lt, is.null))]
    merged <- mergeGraphs(lt)

where allPath represents all organism pathways in kegg.

the nodes of obtained graph are different from those obtained asking
compounds by reaction, m'I missing something?

Additionally, someone know's an automated way to export the graph to
cytoscape, or even to write a KGML?

Thanks in advance

Ricardo

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