Hi Marc, Sorry to hijack the topic. I just wonder if there is any way to create a transcriptDb object using a TCGA GAF file ( https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anony mous/other/GAF/GAF_bundle/outputs/TCGA.Sept2010.09202010.gaf) )? I looked at the devel version of GenomicFeatures package and cannot find any information. Thanks a lot, Ying > Date: Tue, 18 Sep 2012 09:16:06 -0700 > From: mcarlson@fhcrc.org > To: bioconductor@r-project.org > Subject: Re: [BioC] Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer > > Hi Joachim, > > The version of the GenomicFeatures package in the development branch of > Bioconductor has had this functionality since the spring. The new > release scheduled for October 2nd will also have it. > > > Marc > > > > On 09/18/2012 08:36 AM, Bargsten, Joachim wrote: > > Hi all, > > I tried to figure out how to get GFF3 annotation data into a > > TranscriptDb object. So far, I could only find the posts in this thread > > and the proposed solution did not work very well for me. In the end, I > > implemented a "makeTranscriptDbFromGFF3" function myself. For those who > > are interested, you can find my version on: > > > > > > > > > > Joachim > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [[alternative HTML version deleted]]

I see, nice. Thanks for pointing me to the correct package/version. Joachim On Di, 2012-09-18 at 09:16 -0700, Marc Carlson wrote: > Hi Joachim, > > The version of the GenomicFeatures package in the development branch of > Bioconductor has had this functionality since the spring. The new > release scheduled for October 2nd will also have it. > > > Marc > > > > On 09/18/2012 08:36 AM, Bargsten, Joachim wrote: > > Hi all, > > I tried to figure out how to get GFF3 annotation data into a > > TranscriptDb object. So far, I could only find the posts in this thread > > and the proposed solution did not work very well for me. In the end, I > > implemented a "makeTranscriptDbFromGFF3" function myself. For those who > > are interested, you can find my version on: > > > > > > > > > > Joachim > > _______________________________________________ > > 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 >