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Imputes missing values in large-scale high-dimensional phenome data. phenomeImpute contains four variations of K-nearest-neighbor (KNN) methods and was compared with two existing methods, multivariate imputation by chained equations and missForest. The four variations are imputation by variables (KNN-V), by subjects (KNN-S), their weighted hybrid (KNN-H) and an adaptively weighted hybrid (KNN-A). The results show that Imputation of missing values with low imputability measures increased imputation errors greatly and could potentially deteriorate downstream analyses.

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phenomeImpute classification

phenomeImpute specifications

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Command line interface
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Unix/Linux, Mac OS, Windows
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phenomeImpute support


  • George Tseng <>


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Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA; Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA; Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA; Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA

Funding source(s)

This study is supported by NIH R21MH094862, U01HL108642, U01HL112707 and RC2HL101715.

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