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The average proportion of heterozygote genotypes per markers in imputed data set was greater than that of before imputation for both assemblies for all chromosomes.
Corrected for baseline levels, Table 4 shows the results of the multilevel analysis without and with multiple imputation for both role security and therapeutic commitment respectively.
There was no relationship between the amount of heterozygote genotypes before imputation and the amount remaining after imputation for both assemblies.
As expected, the larger the number of genotypes that could be inferred with a probability of one, the higher the quality of imputation for both methods.
When Sets D and E were used as reference and test populations, respectively, imputation accuracy was slightly increased compared to that obtained for within-UK imputation, for both imputation methods (random and BEAGLE) and for all three LDP SNP sets (Table 4).
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70 This will allow imputation both for variables missing for entire studies as well those missing more sporadically.
This is because the marker imputation relies on surrounding markers, whereas the imputation for SNPs at both ends can use information only from one side.
This analysis utilized bayesian imputation for missing data both under an assumption that the missing information was missing at random and under plausible assumptions on mechanisms for informative missingness (see supplementary appendix 1).
We use the average relative error (for continuous variables) and misclassification error (for categorical variables) to assess the imputation performance for both the logistic and random forest models.
The accuracy of the four imputation methods for both continuous and categorical variables are compared in figure 1 for the cirrhosis cohort and HCC model.
MissForest had the least imputation error for both continuous and categorical variables at each frequency of missingness, and it had the smallest prediction difference when models used imputed laboratory values.
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