[BioC] extending GenomicFeatures to makeTranscriptDbFrom other sources (i.e. GFF3)

[Marc Carlson]

Hi Malcolm,

We don't yet support GFF in this way.  But you can always use the very
general makeTranscriptDb() function.  It takes a lot more arguments, and
their values (specifically labeled data.frames) may have to be prepared
a bit more, but it should build a database for you just as the helper
functions for biomaRt and UCSC will do. 

So your options appear to be that you could either read in the gff file
as a data.frame and then chop it into the bits you need to satisfy the
various arguments, or you could opt to directly read in tables/views
from your Chado DB and do the same.  Which of these is more appealing
will probably depend on your comfort levels with R, SQL and the data
source.  But either way I think the answer you need is to look at:

?makeTranscriptDb

If you are feeling enterprising and would like to contribute a
TranscriptDbFromGFF3() or a TranscriptDbFromChado() helper function we
would happily welcome your contribution.  ;)



  Marc



On 02/15/2011 09:08 PM, Cook, Malcolm wrote:
> Hi,
>
> GenomicFeatures can create TranscriptDb from ucsc or from BioMart, which I have used to good effect.  Thanks!
>
> My aim is now to perform an analysis with a specific old version of the flybase supplied fly gene annotations (namely, ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.22_FB2009_09/gff/)
>
> Thus, I would like to have a TranscriptDb populated from this GFF3 (it is also available in Chado, if that helps).
>
> Does anyone have already written and willing to share an adaptor for GFF3 (makeTranscriptDbFromGFF3 ??) , or Chado, or suggest another route for me (write my own?).
>
>
> Thanks,
>
> Malcolm Cook - Stowers Institue for Medical Research
>
>
>   * http://fb2009_09.flybase.org/
>   * ftp://ftp.flybase.net/genomes/Drosophila_melanogaster/dmel_r5.22_FB2009_09/gff/
>   * http://fb2009_09.flybase.org/static_pages/downloads/archivedata3.html
>
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