Oh sorry I missed that little detail about using gene symbols.

Here is how you would do it when you need to query by gene symbol:

library(Homo.sapiens)
cols(Homo.sapiens) ## shows cols you could use
keytypes(Homo.sapiens) ## shows keytypes
k <- keys(Homo.sapiens,keytype="SYMBOL")  ## discovers all available 
keys of this kind
result <- select(Homo.sapiens, k, cols=c("TXNAME","TXSTART","TXEND", 
"TXSTRAND"), keytype="SYMBOL")


The plan to support transcriptsBy etc for OrganismDbi is still just a 
plan.  But we don't intend for it to remain a "plan" forever.


   Marc





On 10/11/2012 01:58 PM, Michael Lawrence wrote:
> 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 
> <mailto: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 <mailto: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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