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Exact(8)
In most cases, joint-family analysis had higher mean prediction abilities than single-family QTL analysis.
The mean prediction abilities within and across families were highest when α=0.0001 and decreased as α increased.
The joint-family method had the highest mean prediction abilities at α=0.0001, ranging from 0.22±0.02 for CL to 0.38±0.02 for SLB.
There was no significant difference in mean prediction abilities for single-family analysis between 1-cM and 0.2-cM resolution maps (Supplementary Figure S3).
Even at the α=0.01 threshold, however, joint-family QTL analysis provided similar or slightly better mean prediction abilities than single-family analysis for all traits.
The mean prediction abilities within families were estimated from single-family and joint-family methods by cross-validation for all traits and for three significance levels (P=0.0001, 0.001 and 0.01) using the 1-cM resolution map.
Similar(52)
As the stringency of the significance level decreased to α=0.01, however, the mean prediction ability of the joint-family method decreased slightly.
The mean prediction ability for each combination of trait, QTL modelling procedure and significance threshold was evaluated as the mean coefficient of determination (Ra) from regression of predicted RIL values on observed RIL values within each single-family validation data set.
The performance of each method was evaluated based on its ability to predict mean HbA1c at 26/28 weeks in each arm (by mean prediction error and RMSE) and on its ability to predict trial outcome expressed as the difference in treatment effect vs. comparator.
Mean prediction error.
The ability of the model to predict point values of PfPR at unsampled locations was quantified using two simple summary statistics: the mean prediction error (MPE) and the mean absolute prediction error (MAPE).
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