Re: [Bioc-devel] OrganismDb: what about BSgenome?
On 06/18/2014 05:26 AM, Michael Lawrence wrote: Would it make sense for an OrganismDb object to have an associated BSgenome? This association is implicit anyway. Or do we need an even broader umbrella object? This would make some things easier. For example, predictCoding(variants, Homo.sapiens). Just nice to have everything in one bundle. Also, could there be a mapping between the genome(variants) ID and Homo.sapiens, so predictCoding(variants) is possible? Or is that just being too automatic? At the very least, it would be nice if the various TranscriptDb methods started to support OrganismDb as an alternative. I know Marc has added many of them already. Which one are missing? My understanding is that most of them actually delegate to the method for TranscriptDb objects. Why not just make OrganismDb extend TranscriptDb so all of them would actually work out-of-the-box (then only override when needed). We could do the same with BSgenome. This looks like a place where multiple inheritance could maybe save us a lot of work. Cheers, H. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] OrganismDb: what about BSgenome?
Sounds nice but we have to be careful. We may need a parameter: Homo.sapiens(hg19) ... because broad adoption of new builds may take considerable time. On Wed, Jun 18, 2014 at 6:13 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 06/18/2014 05:26 AM, Michael Lawrence wrote: Would it make sense for an OrganismDb object to have an associated BSgenome? This association is implicit anyway. Or do we need an even broader umbrella object? This would make some things easier. For example, predictCoding(variants, Homo.sapiens). Just nice to have everything in one bundle. Also, could there be a mapping between the genome(variants) ID and Homo.sapiens, so predictCoding(variants) is possible? Or is that just being too automatic? At the very least, it would be nice if the various TranscriptDb methods started to support OrganismDb as an alternative. I know Marc has added many of them already. Which one are missing? My understanding is that most of them actually delegate to the method for TranscriptDb objects. Why not just make OrganismDb extend TranscriptDb so all of them would actually work out-of-the-box (then only override when needed). We could do the same with BSgenome. This looks like a place where multiple inheritance could maybe save us a lot of work. Cheers, H. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] OrganismDb: what about BSgenome?
Multiple inheritance might work. May be a good time to think about an abstract sequence source, i.e., anything that supports getSeq(). Right now, we use ANY for that, which is not ideal. Same for transcript source. We've already implemented the TxDb API directly on top of biomaRt. On Wed, Jun 18, 2014 at 3:13 PM, Hervé Pagès hpa...@fhcrc.org wrote: On 06/18/2014 05:26 AM, Michael Lawrence wrote: Would it make sense for an OrganismDb object to have an associated BSgenome? This association is implicit anyway. Or do we need an even broader umbrella object? This would make some things easier. For example, predictCoding(variants, Homo.sapiens). Just nice to have everything in one bundle. Also, could there be a mapping between the genome(variants) ID and Homo.sapiens, so predictCoding(variants) is possible? Or is that just being too automatic? At the very least, it would be nice if the various TranscriptDb methods started to support OrganismDb as an alternative. I know Marc has added many of them already. Which one are missing? My understanding is that most of them actually delegate to the method for TranscriptDb objects. Why not just make OrganismDb extend TranscriptDb so all of them would actually work out-of-the-box (then only override when needed). We could do the same with BSgenome. This looks like a place where multiple inheritance could maybe save us a lot of work. Cheers, H. Michael [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel -- 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: hpa...@fhcrc.org Phone: (206) 667-5791 Fax:(206) 667-1319 [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
