This might be really basic, but I am trying to understand why a standardized genotype matrix is constructed this way.
In a standardized genotype matrix we have each ij element:
w ij = (x ij - 2 p i ) / SQROOT( 2p i (1 - p i )
Where x ij is the number of copies of the reference allele for the i SNP of the j individual and p i is the frequency of the reference allele.
I understand that the number of reference allele that any individual can have is influenced by the allele frequency of that SNP, so standardizing it by the allele frequency seems a good idea. But why is it standardized in this way? Is it a common standardization? Does it have a name?