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In genotype imputation of both common and rare alleles, GIGI-Pick substantially outperformed all other methods considered and had the added advantage of incorporating prior linkage information.
The chained equations allow imputation of both categorical and continuous variables, while predicted mean matching restrict imputations to the appropriate range (by matching the predicted value to the closest value in the dataset).
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33 We used both an imputation of mean value and a more complex approach (longitudinal mixed model), which does not impute data in the case of missing outcomes.
We used both an imputation of mean value and a more complex approach (longitudinal mixed model) that does not impute data in the case of missing outcomes.
This is evaluated on a per locus basis, with imputation errors of both the low frequency and the high frequency allele being combined.
Different statistical approaches may be applied to survival modelling, and in the case of this analysis, involved the imputation of survival data for both treatment arms in the BOND study to account for censored values.
The large sample size and number of events, and the use of multiple imputation of missing values, controls for both random and systematic error, and thus enables accurate estimation of associations although ideally there would be no missing values.
To predict genotypes at untyped SNPs in both regions, imputation of the UK1, Scotland 1 and VQ58 data sets was performed using the IMPUTE2 software and the combined CEU 1000 Genomes low-coverage pilot and complete HapMap3 haplotypes reference set, which was filtered to remove duplicate haplotypes (both from https://mathgen.stats.ox.ac.uk/impute/impute_v2.html) (8).ac.uk/impute/impute_v2.html
Only 2 studies (2%) carried out any diagnostic checks of their imputation model, both of which compared the distribution of observed and imputed values.
However, both costs and accuracy of imputation of these strategies are highly sensitive to several factors.
They also suggest competing advantages for the regression tree and Bayesian mixture model approaches, making both reasonable default engines for multiple imputation of categorical data.
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