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thibautjombart / adegenet

adegenet: a R package for the multivariate analysis of genetic markers
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snapclust: hybrids for 3 groups #227

Open markusmoest opened 6 years ago

markusmoest commented 6 years ago

Dear Thibaut, I am interested in using snapclust and because I am working with a system with three parental species and hybrids between them, I was wondering whehter you have plans to extend the hybrids feature to work on 3 groups or more in the near future? As far as I understand it's restricted to two groups for the moment.

Thanks, Markus

thibautjombart commented 6 years ago

Hi Markus At the theoretical level this is easy, but the implementation isn't something I can do in 2 minutes, so it would have to be part of a PR. Only problem here is that if we go down this road, we need to allow for hybrids for any number of parental populations, and the complexity of this problem grows nastily fast. Cheers Thibaut

markusmoest commented 6 years ago

Hi Thibaut, Thanks for your reply. I think I get your point. It would be really great to be able to use snapclust with hybrids with more than 2 groups at some point, however I think I can use a hierarchical approach in my Daphnia case for now because during each of the different time periods I am looking at it's mostly just two of the three groups hybridising. Still I'd be interested in a version modelling hybrids between more groups for some other systems I am working on. I have the impression that there are a quite a few people working on hybridising systems with 3 maybe 4 groups but not many with more than that. So maybe it would be worth to extend the hybrids option to just 3 or 4 groups. Anyway, thanks for your help and developing these great tools! Cheers, Markus