You should change An and Bn to 1 and 2, MATLAB's indexing starts from 1 not zero so everytime i = 2 you'll get an error since An and Bn will be 0.
The values of C come from X, so eventually thats what they should be, C will not equal X exactly but all of it's values come from X. Also these lines are overriding each other in each loop, so technically you are only storing the results from the last loop.
The loop that I gave you will store the values at each full iteration, now I am not sure if what you want is to have the same value for the row and column for each full iteration or not but this will give that meaning that you're not losing any data.
Also I don't know why X has that many numbers in it you are only using X(1,1) or X(2,2) not sure if that's what you want or not.
for cols = 1:2 % # of cols in matrix for genome prediction
C(:,cols) = X(An, Bn);
end
C(rows, :) = X(An, Bn);
to store each loop you should use this
for cols = 1:2 % # of cols in matrix for genome prediction
C(rows,cols) = X(An, Bn); % this will not override and will store the values of each loop
end
