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
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