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Imputation of the remaining non-genotyped sires was difficult because they had few progeny and because most dams of their progeny were not genotyped.
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Even with the choice of a rare-cutter enzyme, the threshold of less than 20% missing data that we applied to determine whether to keep a marker in the dataset led us to remove a large number of markers and implied imputation for the remaining scattered missing data.
Imputation of remaining missing values: remaining missing values were imputed using sequential K-nearest neighbor (SKNN) imputation (Kim et al., 2004 ) with k =5.
Based on the sequence data for the subset of the study participants, we wish to impute untyped markers for the remaining subjects using current genotype imputation methods.
There was no imputation for missing data for the remaining ACR components.
There was no relationship between the amount of heterozygote genotypes before imputation and the amount remaining after imputation for both assemblies.
Plots of the estimates obtained using the cold deck imputation procedure against those obtained from the remaining procedures have a similar appearance to Figure 3.
The estimated maximum communality is the R2 of one individual measure on the remaining 92 measures or in other words the imputation equation.
For the remaining genes, the value of a flagged spot was imputed using K nearest neighbors' imputation as implemented in the R-package "impute".
Because the imputation method relies on LD between SNPs on the LDP and the remaining SNPs on the high-density panel, the choice of SNPs for the LDP also affects the accuracy of imputation.
With respect to the remaining data missing values were imputed using multiple imputation.
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