KEGGREST: restricting pathways of compounds to certain organisms

Question

[pixie@bioinfo]

I am using KEGGREST package to obtain the pathways of certain compounds. For e.g:

> library('KEGGREST')
> keggGet("C02094")[[1]]$PATHWAY

Output:

                map00830                       map00906
     "Retinol metabolism"      "Carotenoid biosynthesis"

I am working on the organism: Solanum lycopersicum (tomato), code: sly. The pathway 'retinol metabolism' is not present in tomato, but 'carotenoid biosynthesis' is present. How do I impose this condition in my script?

Thanks

[Greg Medlock]

As far as I am aware, you cannot filter results from a get command prior to actually performing the REST call. In other words, a get command will always return all of the information for the corresponding entry in the databse you queried. You will need to make the call then filter the REST output using whatever information you have regarding pathways present in Solanum lycopersicum. Posting the format of this would be useful.

[pixie@bioinfo]

Thank you for the suggestions. I just checked that the url: http://rest.kegg.jp/list/pathway/sly links to a page with the list of sly-pathways. I can see that sly00906 (instead of map000906) is present but map00830 is not. However, I am unable to formulate the command corresponding to the link above using keggList(). Any help will be greatly appreciated.

[pixie@bioinfo]

Oh, got it. Just tried out this keggList("pathway","sly").