[R] Genotypes are not all the same

[Gregor Gorjanc]

Farrel Buchinsky <fjbuch <at> gmail.com> writes:
> Clearly g1 and g2 are not exactly the same even though they are the same
> class.
> I can make g2 behave as g1 if i type
> g3<-genotype(g2)
> g3 then behaves as it should.
> 
> The issue may have arrisen since g2 is just a subset of a much bigger object
> that was created using reshape command in the base package or maybe melt and
> cast in the reshape package. Can anyone enlighten me?

genotype class behaves internally much like factor class. I guess that
levels/alleles were dropped somewhere. You have to figure out where this 
happened.

Gregor