[Bioc-devel] naming of TxDb packages

Hervé Pagès hpages at fhcrc.org
Thu Nov 3 19:19:11 CET 2011

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


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.


> Thanks,
> Michael
> 	[[alternative HTML version deleted]]
> _______________________________________________
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Hervé Pagès

Program in Computational Biology
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