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Such models can be used to make predictions for model performance assessment, but the task is made more complicated by the multiple imputation structure.
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For the final genotype imputation, the haplotype structure of the reference population is used.
Impute: impute: Imputation for microarray data.
Using large datasets with minimal population structure for imputation and GS is advocated to avoid heterogeneity of imputation and GS accuracies across subgroups of individuals.
Quality of imputation under different population structures was assessed.
This chapter reviews methods of extrapolation, focusing on gradient imputation, which preserves the covariance structure of models at their original scale.
A repeat factor analysis using the subsequent values after imputation demonstrated the same factor structure and similar factor loadings.
The ERF study is more robust for this kind of error since it benefits from the family structure in the imputation.
When using whole-genome sequence data, differences in extent of LD and population structure may affect imputation accuracies more in crop or livestock analyses than in human analyses.
Thus, for genomic prediction, the addition of animals with phenotypes and imputed genotypes to the datasets increases accuracy also, although the magnitude of this improvement depends on heritability of the trait, imputation accuracy, and size and structure of the population [ 4- 6].
This method has the advantage over ad hoc single imputations because the appropriate error structure is maintained.
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