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
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Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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