Linkage disequilibrium estimation

On Nov 21, 2016, at 06:27 , Felipe Hern?ndez <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