function r = est_rec_fracs(geno)
%estimate adjacent pairwise recfracs in a genotype array
%
%Copyright notice
%this code was written by Gary Churchill who retains all rights.
%If this code to generate results in publications please cite
%Sugiyama F, Churchill GA, Higgins DC, Johns C, Makaritsis KP, Gavras H, Paigen B (1999)
%Quantitative trait loci analysis of blood pressure in mice on a high salt regimen:
%Concordance with rat and human loci. Submitted to Nature Genetics.
%

m = size(geno,2);
r = zeros(m,m);		           % array of rec fracs
cnt = [0 1 2; 1 0 1; 2 1 0]; 

if max(geno(:)>1)
   F2 = 1;
else
   F2 = 0;
end

for i = 1:m-1
   for j = i+1:m
   	M = geno(:,[i,j]);		%pull two adjacent rows out of geno
   	M(any(isnan(M)'),:) = [];	%remove rows with missing values
      r(i,j) = sum(diag(cnt(M(:,1)+1, M(:,2)+1)));	%count crossovers
      if F2
         r(i,j) = sum(M(:,1)~=M(:,2));
         r(i,j) = r(i,j)+ sum((M(:,1)==0 & M(:,2)==2) | (M(:,1)==2 & M(:,2)==0));
      else
         r(i,j) = sum(M(:,1)~=M(:,2));
      end
      
      %normalize
      if F2	%backcross
        r(i,j) = min( r(i,j)/(2*size(M,1)), 0.5);
      else %f2  
         r(i,j) = min( r(i,j)/size(M,1), 0.5);
      end
   end
end

%symmetrize
for i = 2:m
   for j = 1:i-1
      r(i,j) = r(j,i);
   end
end