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The average performance of classifiers has been listed based on the imputation by K-nearest neighbor (Knn = 1, Knn = 3, Knn = 5, and Knn = 7), mean, and medoid, respectively.
The variance ratio for a particular SNP is a ratio of the empirically observed variance (based on the imputation) to the expected binomial variance p 1-p), where p 1-pthe minor allele frequency[18].
The "best guess" genotypes based on the imputation were used in the analysis.
A comparison between all imputation approaches was done based on the imputation quality metric (R) calculated by the MaCH tools.
Results based on the imputation model seem to be robust to modest departures from the assumptions of missing at random behind the imputation, based on sensitivity analyses.
However, the cause-specific estimates that are based on the imputation model can be interpretable as estimates of net survival only if it is reasonable to assume independence between prostate cancer death and death from other causes than prostate cancer.
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The results based on the imputations are only valid if the data were MAR, and we had specified appropriate imputation models.
Missing post-baseline scores were imputed based on last observation carried forward (LOCF) or based on the multiple imputation approach if data were not available for LOCF for the third primary efficacy endpoint.
Additionally, when we apply the FE-estimator, we find a parameter estimate of 0.376 based on the multiple imputation strategy, which resembles the results from the main sample but is not significant at conventional levels (α = 0.152).
Descriptive statistics were based on the first imputation.
These p-value thresholds are useful reference for GWAS based on the genotype imputation using genotypes from HapMap and 1000 Genomes as reference sample.
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