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Additionally, contacts in the countries for which out-of-sample imputation was undertaken suggested that the imputed values had face validity.
The incomplete form was available in three alternative imputations: a "hard" imputation, a "dosage" imputation, and an ensemble of 100 sampled imputations that constituted a single "multiple" imputation set (these imputations being generated by fastPHASE [Scheet and Stephens, 2006]).
Since race was missing on 17% of the retrospective sample, single imputation of race was done using a baseline-category logit regression using costs and patient and hospital level variables as described above as predictors.
The HapMap phase II CEU data [NCBI build 36 (UCSC hg18)] was used as the reference sample for imputation using MACH software.
At 12 months' follow-up, using the full sample including imputation for missing cases, the proportion of participants who had not harmed themselves over the preceding six months was slightly higher for the group therapy (41.9%) than for routine care (38.9%, table 2).
To determine the effect of this sampling on imputation accuracy, SNPs were progressively sampled from the entire set based on the proportions predicted by the SNP yield curves and their imputation statistics were tabulated.
The authors found that for most of the studied samples, mixtures from at least two HapMap reference samples maximized imputation accuracy [ 16].
The recovery process is based on the following simple iterative procedure (Yaroslavsky et al. 2009 ): Algorithm 1. Discrete sampling theorem imputation algorithm.
The final sample post-imputation for this investigation consisted of 3,105 respondents.
Exon pilot data in the 55 CEU samples without imputation for tag SNP analysis was denoted by EXON.
We created 6,105 in silico intercross samples by imputation of genotypes for all pairwise combinations of 111 M.
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