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]]
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