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. 2019 Jan 23;211(3):1105–1122. doi: 10.1534/genetics.118.301851

Table 4. Prediction accuracies of whole genome Additive and Pairwise epistasis using {− 1,1 } coding, along with the Homeo, Within, and Across genome marker sets for both {− 1,1 } and { 0,1 } marker coding using the LAVHAE marker orientation.

LAVHAE Additive Pairwise Homeo−11 Homeo01 Within−11 Within01 Across−11 Across01
GY 0.601a 0.604 0.606 (167%)b 0.599 (–67%) 0.627 (867%) 0.600 (–33%) 0.630 (967%) 0.604 (100%)
PH 0.559 0.637 0.606 (60%) 0.580 (27%) 0.652 (119%) 0.570 (14%) 0.650 (117%) 0.584 (32%)
TW 0.515 0.576 0.560 (74%) 0.516 (2%) 0.596 (133%) 0.514 (–2%) 0.581 (108%) 0.525 (16%)
HD 0.664 0.712 0.692 (58%) 0.682 (38%) 0.710 (96%) 0.674 (21%) 0.722 (121%) 0.682 (38%)
a

Mean Pearson correlation between predicted and observed genetic values across 10 random 5-fold cross-validation replications.

b

The percentage of the nonadditive genetic predictability as relative to the Pairwise model is shown in parentheses (Equation 4).