Haplotype association in case-control study with R

Question

[mel22]

Hello, Please what do advice me to perform haplotype association test on a sample of 1000 observation with R. I tried to use Haplostats but it's very slow and always crush.

I tried to use beagle data converted with pseudomarker program, but I don't know how to use it in R.

Can you help please ?

Thank you