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. Michael [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel