Imputing missing genotypes with weighted k nearest neighbors

Abstract

Missing values are a common problem in genetic association studies concerned with single nucleotide polymorphisms (SNPs). Since most statistical methods cannot handle missing values, they have to be removed prior to the actual analysis. Considering only complete observations, however, often leads to an immense loss of information. Therefore, procedures are needed that can be used to replace such missing values. In this article, we propose a method based on weighted k nearest neighbors that can be employed for imputing such missing genotypes.