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The limitation was that some of the imputed SNPs had suboptimal imputation quality, which translates into measurement error affecting both SNP-based and haplotype-based analyses.
The majority of the imputed SNPs had a high imputation quality score (MACH-R> 0.6).
All of the imputed SNPs had a high imputation quality score.
These statistics provide a very complete validation set of the imputed data, which assures the coherence of the imputed values regarding the collected data from donors.
We chose not to report the imputed dataset here because the findings of the imputed data set concurred with the complete case analysis.
The imputation step followed by an estimation of the imputed data set was repeated six times for each data set.
Final imputed values are the exponentially transformed values of the imputed logarithmic values (Hertz-Picciotto et al. 2005; Little and Rubin 2002; Shumway and Stoffer 2000).
However, the imputation approach may be limited by the low accuracy of the imputed rare variants.
Thus, the increment in imputation quality was largest when the minor allele frequencies of the imputed variants were below 1%%.
While the answer lies in the intended use of the imputed genotypes, it would be useful to have some generic assessment of imputation performance.
In this section, we focus on our analysis of the imputed datasets.
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