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Last observation carried forward (LOCF) was used for imputation of missing data.
Multiple regression was used for imputation of missing data with predictive values based on age, sex, race, and adherence.
The LOCF was used for imputation of missing data, and pain scores obtained after rescue medication were considered missing for the primary efficacy analysis.
The software package Beagle (version 3.3, [ 13]) with default settings was used for imputation of missing marker genotypes and for phasing the genotypes.
Briefly, MACH version 1.0.16 software was used for imputation of genotype data obtained by the GWAS of RA with the Hapmap phase II East Asian panel (JPT and CHB) as reference.
However, if the reference population used for imputation of crossbred animals was replaced by a pure breed population, both correct rate and correlation coefficient decreased dramatically by about 0.10 and 0.25, respectively.
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Several factors influence the accuracy of imputation and our objective was to investigate the effects of the size of the reference population used for imputation and of the imputation method used and its parameters.
The Beagle software program was used for imputation and accuracy of imputation was assessed based on the Pearson correlation coefficient between observed and imputed genotypes.
We implemented two separate imputation experiments that differ in the size of the high-density reference panel used for imputation: (1) a reference panel of 128 Yorkshire haplotypes or (2) a reference panel combining the 128 Yorkshire haplotypes with the haplotypes of all animals that are part of the training panel (~1700 additional haplotypes) in the respective cross-validation dataset.
Additional file 2. Number of SNPs used for imputation.
Furthermore, significantly CPAANN turned out to be the best in the class of AANN architectures used for imputation.
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