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For dealing with missing values in microarry dataset, the overall imputed ratio by KNN algorithmis about 34% see Additional file 1.
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Overall, IMPUTE 2 has demonstrated superior imputation accuracy in most comparative studies (8, 11).
Overall, we imputed values for 35% of records in the cohort study and 11% of records in the GP presentation study.
41 42 Overall, data were imputed for 68 participants (8.0%) with a maximum of three covariate values imputed for any one participant (table 3).
For each of the two outcomes (breast cancer-specific mortality and overall mortality), 50 imputed datasets were generated and results were combined using the PROC MI and PROC MIANALYZE commands in SAS (version 9.3) with appropriate correction for variance.
Overall, M = 5 imputed data sets were generated.
Using the program SNPEff [ 42], we imputed the overall impact of all variants as largely modifying (82.1%), followed by low (11.7%), moderate (5.82%) and high impact (0.395%).
In sensitivity analyses, we imputed the overall median follow-up time of 1.35 years for each subject lost to follow-up before reaching median follow-up time; and varied assumptions around number of diarrhoea episodes.
However, accuracy of genomic evaluation decreased in comparison with the reference scenario when genotypes were imputed with lower overall accuracy (R = 0.88).
Overall, 22.97% of women and 29.88% of men had either smoking or body mass index imputed by multiple imputation (data were not imputed for ethnicity all patients with missing ethnicity were treated as white/not recorded).
IMPUTE2 metrics for internal cross-validation of existing sample genotypes against imputed values indicated that imputation was successful (>95% overall concordance; Supplemental Table 1).
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