Our estimates of mean allelic error of imputing up to 50K from evenly spaced 3K panel (2.8%) were lower compared to Bovine3K (3.3%) which may be because of the higher number of SNPs with higher MAF in evenly spaced 3K SNP panel.
The respective mean allelic error rates of imputing 50K specific (1324 SNPs) genotypes are 2.75%, 2.75% and 4.55%.
The mean allelic error rates of imputing 50K specific (1324 SNPs) genotypes are 2.85%, 3.15% and 4.25% when 25%, 50%and75%5% of animals, respectively, are in the test set.
The mean allelic error rates of imputing SNP genotypes between different SNP chips obtained with IMPUTE2 are presented in Table 3.
The mean allelic error rate of imputing up to 800K decreases from 4.78% in the 2-tiered approach to 4.62% in the 3-tiered when Bovine3K SNP panel are used in the test animals.
The mean allelic error rates of imputing 15K specific (205 SNPs) genotypes are 0.80%, 0.95% and 1.40% when 25%, 50%and75%5% of the animals, respectively, are in the test set and the remainder of the animals with genotypes on 1529 SNPs (15K+50K) in the reference set.
For Townsend score and distance alike, the difference between the actual mean in the injured and the mean of randomly imputed values in those not injured is approximately correct to adjust for in the subsequent multivariate analysis, and the process incorporates the appropriate degree of variation at individual level.
The problem of localizing errors by means of edits and imputing erroneous fields is known as the edit-imputation problem and solutions to that date back to mid-1970s [17]. mid-1970s [17]
The few missing values in predictors were imputed by means of single imputation (SI, in R language: aregImpute, n.impute = 1, type = ' pmm').
Maximally six missing values on each questionnaire were allowed, and these values were imputed by means of single imputation using expectation maximization techniques [ 28].
