We're actually using a patched version of makeTranscriptDbFromBiomart to
get models out of an internal biomart.  Patch is on its way to Marc.

So it would be like: TxDb.Hsapiens.BioMart.hg19.gneGenes?

Seems weird to mix the technical mode of data retrieval into the name.

Michael

2011/11/3 Hervé Pagès <hpages@fhcrc.org>

> Hi Michael,
>
>
> On 11-11-02 08:58 PM, Michael Lawrence wrote:
>
>> What are the precise meanings of the tokens in the TxDb package names. In
>> particular, is "UCSC" the genome provider or the annotation provider? In
>> the official packages, those are one in the same, but if someone wanted to
>> make a package for custom annotations on a UCSC genome?
>>
>
> The pkg name is generated automatically by internal helper function
> GenomicFeatures:::.**makePackageName(). This function extracts all the
> tokens from the txdb's metadata table. It looks like the 3rd token
> in the pkg name is extracted from the 'Data source' field and can only
> be "UCSC" or "BioMart", typically indicating whether the txdb was made
> with makeTranscriptDbFromUCSC() or makeTranscriptDbFromBiomart().
> The first function downloads annotations from the UCSC genome
> browser using rtracklayer. The 2nd one downloads them with biomaRt
> from whatever mart/dataset was specified.
>
> For your custom annotations, the final name of the pkg will depend on
> what GenomicFeatures:::.**makePackageName() finds in the metadata
> table of your txdb, but, if 'Data source' is not "UCSC" or "BioMart",
> it seems that GenomicFeatures:::.**makePackageName() will fail (and not
> in a very informative way I'm afraid). If I understand correctly, you
> are making your custom txdb object with a call to makeTranscriptDb()?
> If that's the case, make sure you provide enough information
> thru its 'metadata' argument. Maybe you could set 'Data source' to
> "UCSC" and use some kind of custom name for the table (which in your
> case is probably not a real UCSC "table"). This custom name will become
> the last token in the package name. So you would end up with something
> like:
>
>  TxDb.Hsapiens.UCSC.hg19.**GenentechGenes
>
> This solution would have the advantage of having
> GenomicFeatures:::.**makePackageName() work out-of-the-box.
> But maybe it's confusing because it suggests that
> the txdb was made with makeTranscriptDbFromUCSC()? I hope
> it's not.
>
> H.
>
>
>> Thanks,
>> Michael
>>
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>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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