TY - JOUR
T1 - Linkage Disequilibrium Between Loci With Unknown Phase
JF - Genetics
JO - Genetics
SP - 839
LP - 844
DO - 10.1534/genetics.108.093153
VL - 182
IS - 3
AU - Rogers, Alan R.
AU - Huff, Chad
Y1 - 2009/07/01
UR - http://www.genetics.org/content/182/3/839.abstract
N2 - Linkage disequilibrium is often measured by two statistics, D and r, which can be interpreted as the covariance and the correlation between loci and across gametes. When data consist of diploid genotypes, however, gametes cannot be identified. A variety of iterative statistical methods are used in such cases, all of which assume random mating. Previous work has shown that D and r can be expressed as covariances and correlations across diploid genotypes, provided that mating is random. We show here that this result also holds approximately when mating is nonrandom. This provides a means of estimating these parameters without iteration and without assuming random mating. This estimator is nearly as accurate as the widely used EM estimator and is many times faster.
ER -