AlphaImpute with phasing, which used the haplotype library, resulted in more correctly imputed genotypes per individual but also in more incorrectly imputed genotypes per individual, which led to a lower animal-specific imputation accuracy than segregation analysis (Table 3).
First, I use an additional national representative sample to better approximate the actual fathers' birth cohorts so that fathers' missing permanent earnings are more accurately imputed.
In a genome-wide context, ℙ(C1) can be viewed as the fraction of sites in the genome that are more accurately imputed by the internal reference panel than by the external reference panel.
In addition to physical injuries and sexually transmitted diseases, which can be more easily imputed to aggression, other disorders such as depression, suicide, drug abuse, delayed beginning of prenatal care and preterm birth have been associated with maltreatment of women [ 3].
Data from further studies of parasite physiology will be useful for refining the imputation model, to incorporate additional variation and more accurately impute lowly expressed genes.
We also created an additional 25(OH D category variable of <25, 25 74.9 and ≥75 nmol/l to summarize the effect size and repeated analyses for model 3. Missing information on the lifestyle factors (n = 514 with missing information on one or more factors) was imputed using the multiple imputation chained equations [47].
Because more genotypes were imputed when offspring were genotyped, there was also more chance that they were imputed incorrectly and, therefore, the percentage of incorrectly imputed SNPs was higher with genotyped offspring.
Zhang et al. (2013) showed, using simulated sequence data and data from the 1000 Genomes Project, that by using the maximum-PD panel, higher imputation accuracy is obtained, and more sites are imputed as polymorphic in the sample population, than if the reference panel consists of randomly selected haplotypes.
