[BioC] Creating annotation packages

[Gábor Csárdi]

Sean, looks great, thanks, G.

On Fri, Jan 30, 2009 at 5:22 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>
>
> On Fri, Jan 30, 2009 at 11:13 AM, Gábor Csárdi <Gabor.Csardi at unil.ch> wrote:
>>
>> Dear All,
>>
>> I am trying to create an annotation package that contains predicted
>> miRNA targets, basically it would be a mapping between Entrez Gene IDs
>> and miRNA families, for a couple of organisms, together with some
>> additional info or course.
>>
>> I am trying to make use of the AnnBuilder package, but could not find
>> out whether it can do this at all or not. Btw. the vignettes of it
>> seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not
>> public any more.
>>
>> So my questions are:
>>
>> 1) Is AnnBuilder the right tool for this?
>>
>> 2) If not, are there any "right" tools? I don't mind creating the
>> sqlite database by hand, but how do I create AnnDbBimap objects for
>> it?
>>
>> 3) Are your scripts for building the standard annotation packages
>> (e.g. org.xx.eg.db) publicly available somewhere? It would be of great
>> help to see how this is done.
>
> Hi, Gabor.  Actually, the AnnBuilder way of building things is deprecated.
> You will want to use the AnnotationDbi package and refer to the SQLForge
> vignette.
>
> Hope that helps.  If you have more specific questions, be sure to include
> sessionInfo() output.
>
> Sean
>
>
>



-- 
Gabor Csardi <Gabor.Csardi at unil.ch>     UNIL DGM