[BioC] KEGG orthology linking (K numbers )?
mcarlson at fhcrc.org
Thu Aug 12 23:22:54 CEST 2010
Because you asked about them, I exposed some more of the KEGG SOAP api
and added 6 new functions to the KEGGSOAP package to help expose the
KEGG ko numbers etc.. I think that these will probably help with your
problem but I cannot be completely sure since you didn't say exactly
what you wanted to do. To use them you will need the devel version of
KEGGSOAP which should update for biocLite() in the next 24 hours or so.
On 08/12/2010 03:58 AM, Vincent Carey wrote:
> The keggorthology package supplies some of the relevant material. See the
> vignette for indications of its scope; post back to the list if there are
> points that are unclear. KEGG.db will supply additional resources. The
> direct association you seek may require some programming. Remember that the
> specific pathway EC numbers are organism-specific, so "hsa" prefix may need
> to be added to certain non-specific tokens, if the application is for Homo
> sapiens, for example.
> On Thu, Aug 12, 2010 at 6:38 AM, Fabian Grammes <fabian.grammes at nofima.no>wrote:
>> Dear List
>> Is there currently any package (or way) allowing to associate KEGG K
>> numbers (K02995) to pathways (ko03011) or ec. numbers?
>> Thanks, Fabian !
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