Marc, Thanks for the complete reply.. Since my original post I've explored the code a bit and see the general approach should not be too hard. I will probably try and contribute makeTranscriptDbFromGFF3 (which I happend to notice mentioned in the project's TODO file ;). I have been using the existing ucsc adaptor to excellent effect, however with a slightly different version of fly genome annotation, and I will write makeTranscriptDbFromGFF3 once the rest of my analysis is fully coded when I will want to make sure I am running against identical annotation set as another convergent analysis used. Cheers, Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA > -----Original Message----- > From: bioconductor-bounces at r-project.org > [mailto:bioconductor-bounces at r-project.org] On Behalf Of Marc Carlson > Sent: Tuesday, February 22, 2011 12:04 PM > To: bioconductor at r-project.org > Subject: Re: [BioC] extending GenomicFeatures to > makeTranscriptDbFrom other sources (i.e. GFF3) > > 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_FB200 > > 9_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 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >