Hi all, this may not be the right place to ask this type of question, if someone could point me to a better place to ask I would appreciate it.
I've been reading papers that do genome wide association analyses between SNPs and various traits in dogs. In it, they do a breed permutation procedure (i.e they permute the phenotypic values per breed, not per individual, re-do the genome-wide association study and see how often the P value is lower than that of the permuted data).
My question is: they say that this permutation method is a way of identifying snp-phenotype traits while accounting for the extreme population substructure found among dog breeds. I'm struggling to understand specifically how a breed permutation analysis could account for population substructure.
If someone could explain it to me in basic terms, perhaps with an example, I would appreciate it.