[R-sig-genetics] Linkage disequilibrium estimation

[Zhian Kamvar]

> On Nov 21, 2016, at 06:27 , Felipe Hernández <fhernandeu at uc.cl> wrote:
> 
> On the other hand, I wonder is there is another package to test LD between
> several multi-allelic loci at the same time (not only two loci)? Thanks for
> your feedback!

Hi Felipe,

There IS another method that can test LD between several loci. The index of association is a measure of multilocus linkage disequilibrium [0] and is implemented in the poppr R package with the function ia(). You can use it on a genind object, which can be converted from loci with the function loci2genind().

Best,
Zhian

[0]: http://onlinelibrary.wiley.com/doi/10.1046/j.1471-8278.2000.00014.x/abstract