function cv = covpairpermute(y, cov, geno, chrid, nperm)
%permutation test for covpairwise
%to test effects of marker pairs that interact with a covariate
%
%Input Variable:
%     y: nxk matrix of trait values
%   cov: nx1 vector of covariates,  use [] if none
%  geno: nxm genotyping array, encoded as 0-1 or as 0-1-2
% nperm: number of permutations
%OUTPUT VARIABLES
%  cv: 4x4matrix of critical values (.8, .9, .95 and .99) from permutation analysis

%missing data check
if any(any(isnan(geno)))| any(isnan(cov)) | any(isnan(y))
   exit('missing data in geno, yy or cov')
end

%permutation test
Fmax = zeros(nperm,4);
for j = 1:nperm
   
   %generate the permutation indices
   ord = randperm(length(y));
   
   %permute the trait values and covariate
   ptrait = y(ord);
   pcov = cov(ord,:);
   
   %compute overall F and record the maximum value
   [F1, F2, F3, F4] = covpairwise(ptrait, pcov, geno, chrid);
   Fmax(j,:) = max([F1(:), F2(:), F3(:), F4(:)]);
end

%sort maximal F's
Fmax = sort(Fmax);

%compute critical values 
cv=Fmax([ceil(.8*nperm),ceil(.9*nperm),ceil(.95*nperm),ceil(.99*nperm)],:);