[BioC] Problem using KEGGSOAP: multiple genes per identity

[January Weiner]

Dear all,

I have hit a wall when trying to get KEGG pathway maps colored by gene
expression. On several of these, an entity on the map corresponds to
several genes. I assume that the entity corresponds to one kegg
orthology ID (at least that is what I observe in the pathways that I
use).

Now I face the following problem: KEGG API does not seem to have a
consistent behavior when multiple genes with different colors are
submitted to the color_pathway_by_objects.

One way would be to use the get_elements_by_pathway SOAP call, since
it returns a mapping between the graphical elements of a pathway and
the genes in question. However, this does not seem to be implemented
in KEGGSOAP.

What do you do in such a case?

Kind regards,
j.

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