Just very simple question. When we calculate LD, we need P(A),P(a),P(B),P(b) and then
However, for raw SNPs or mutation, P(A) or P(B) might be 0. In such situation, r can not be calculated. Is there any compromised way to calculate r or D' for such situation?
In another way, suppose I only observe 1 haplotype for 2 loci in all the samples (very large samples)? Can I take the such as as completed linkage or I can take record LD as 'NA'?