It's definitely a step in the right direction. A small next step would be
supporting queries based on gene symbols, as the OP had asked about. Sure,
one could do a transcriptsBy() on the TxDb package and subset, but that
means it has to be by="gene", and it's slower. Also, has there been any
progress towards supporting transcriptsBy on the OrganismDbi package?

Michael

On Thu, Oct 11, 2012 at 1:46 PM, Marc Carlson <mcarlson@fhcrc.org> wrote:

> Yes,
>
> Sorry about the lack of memos.  ;)  OrganismDbi is a new package that
> allows you to make meta packages from annotation packages that implement a
> select() method.  Homo.sapiens is one we made for humans.  It combines the
> human org package, the hg19 txdb known gene package and the GO.db package.
>  The package does not actually "contain" all of that data though.  It just
> retrieves it as requested and returns it to users as if there was a single
> place it was all coming from.
>
>   Marc
>
>
>
>
> On 10/11/2012 12:33 PM, Steve Lianoglou wrote:
>
>> On Thu, Oct 11, 2012 at 2:54 PM, Tim Triche, Jr.<tim.triche@gmail.com>
>>  wrote:
>>
>>> OrganismDbi -- too many of us are used to doing things the confusing way
>>> --
>>> using OrganismDbi packages like Homo.sapiens will be better long-term
>>>
>> Cool ... I like being less confused.
>>
>> Thanks for the pointer,
>> -steve
>>
>>
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