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The effect of MAF of imputed SNPs on imputation reliability is shown in Figure 6, with a Michaelis-Menten curve fitted for each scenario separately.
Multiple imputation is also employed to assess the uncertainty due to imputation since results based on imputation alone, especially when linking imputed locations to other spatial data, may be questionable.
The skewed distribution at high doses was maintained no matter the limitation placed on imputation percentage (PDI) in 15 imputed data sets (results not shown).
Most of these changes did not have a major influence on imputation accuracy or the number of imputed SNPs passing the probability threshold (Table 3).
We set this constant to one as adding different values has little effect on imputation performance (Supporting Information, Table S1 and File S1).
We measured each method's impact on imputation by computing the MSE and Pearson correlation coefficient (r) between the imputed z-scores and true z-scores.
Hence, we only focus on imputation with decorrelated models.
Coverage was calculated using an approach based on imputation and cross validation.
However, removing SNPs from the target set based on imputation coverage is more efficient than pairwise tagging.
The framework exploits a recurrent neural network topology, the so-called state-space neural network (SSNN), with preprocessing strategies based on imputation.
We compared two methods that are based on imputation methods with regard to the bias and root mean square error (RMSE) of population parameters.
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