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In order to minimize the amount of imputation stratification between samples, we selected the SNPs from the GoNL reference set that were present either on one or both genotyping platforms (Illumina or Affymetrix, N = 989,757) using VCFtools (Danecek et al. 2011).
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There was no relationship between the amount of heterozygote genotypes before imputation and the amount remaining after imputation for both assemblies.
The predicted survival probabilities were unaffected by the amount of missingness or the imputation approach applied.
A simulation study showed that multiple imputation performed well, even in the presence of a large amount of MVs and using an imputation model including only CES-D items.
Moreover, the differences between SMI and MMI were negligible (the main effect of imputation method failed to account for a substantial amount of variance in the bias of the subpopulation differences and the regression coefficient β2).
Percentages of alleles missing before and after imputation indicated the amount of fill needed and remaining.
To address the modest amount of missing data, we used multiple imputation on the set of independent variables.
Web appendix A gives further details of the imputation approach, the amount of missing data, and the results of sensitivity analyses.
As body mass index, smoking status and Townsend deprivation score may be important confounders and have a certain amount of missing data, we used multiple imputation for the missing values[ 35, 36].
Imputation reduces the amount of sequencing and data storage required, though the study found that fewer null mutations were detected in the imputed data set suggesting that some mutations were missed in these individuals.
Due to the significant amount of missing data, MICE-CART multiple imputation was conducted before running survival analysis.> -wrap-foot> aAll causes of death; bAmong those with at least one CD4 exam; cAmong those with at least one viral load exam; SISCEL National Database for Laboratoryy.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com