Starting with a 3x3 matrix, three potential haplotypes 2x2 matrices will be calculted and evaluated. The most likly one is choosen. A dicrete solution values are not enforced. This reduces increases the right prediction on real data.
1  findoptimal(A, B, C, D, mmorg, exact = 1e05)

A 
Firts entry of the 2x2 matrix. 
B 
Second numeric entry of teh 2x2 matrix. 
C 
Third numeric entry of the 2x2 matrix. 
D 
Last numeric entry of the 2x2 matrix. 
mmorg 
3x3 matrix of the pair of original snip pairs. 
exact 

It chose the 2x2 model of haplotypes with the smallest prediction error.
AA 
Coefficient of x^3 
BB 
Coefficient of x^2 
CC 
Coefficient of x 
DD 
Coefficient of the intercept 
Jan wolfertz
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