[BioC] GenomicFeatures: makeGeneDbFromBiomart()

[Marc Carlson]

Hi Guido,

If you just want gene information, then the
makeTranscriptDbFromBiomart() function should already give you gene IDs
affiliated with the transcripts along with grouping information in
convenient GRangesList objects.  Yes, this database is focused on the
transcripts and their components, but it is not meant to be isolated
from proper gene IDs.

And if you want to then link that information to more classic
gene-centric annotations then you might want to look at something like
the org.Hs.eg.db package (which includes IDs for ensembl IDs).

Using these two resources together, our hope was that it should be
possible to do a large number of meaningful things.  So what
specifically was it that you needed to do?


  Marc


On 03/01/2011 02:56 AM, Hooiveld, Guido wrote:
> I noticed that the library GenomicFeatures provides a set of very powerful functions to create databases with transcript-centered annotations from e.g. the BioMart database (makeTranscriptDbFromBiomart).
> I was wondering whether a function could be added that will allow the build of a gene-centered annotation database? E.g: 'makeGeneDbFromBiomart()' and/or 'makeGeneDb'.
> I am asking because I would like to easily retrieve AND store the annotation info of all Ensembl mouse genes. I already had a look at the source code to see whether I could modify some parts of the code myselves to create such function, but to me the code is too complicated to feel comfortable adapting it, but i have the *feeling* that this is rather straight-forward for the more knowledgable R-gurus, hence my question.
>
> Thanks in advance for considering,
> Guido
>
> ------------------------------------------------
> Guido Hooiveld, PhD
> Nutrition, Metabolism & Genomics Group
> Division of Human Nutrition
> Wageningen University
> Biotechnion, Bomenweg 2
> NL-6703 HD Wageningen
> the Netherlands
> tel: (+)31 317 485788
> fax: (+)31 317 483342
> email:      guido.hooiveld at wur.nl<mailto:guido.hooiveld at wur.nl>
> internet:   http://nutrigene.4t.com<http://nutrigene.4t.com/>
> http://www.researcherid.com/rid/F-4912-2010
>
>
>
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