On Fri, Jan 30, 2009 at 11:13 AM, Gábor Csárdi <Gabor.Csardi@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 seem to a bit outdated, e.g. the 'writeAnnData2Pkg' function is not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

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