slideimp: efficient imputation of DNA methylation data.
SUMMARY: We developed slideimp, an R package that extends and optimizes K-nearest neighbor (K-NN) and Principal Component Analysis (PCA) imputation with grouped and sliding-window modes for accurate and efficient imputation of microarray and whole-genome DNA methylation (DNAm) data, respectively. Under a realistic scenario, slideimp achieved ≈12-28× faster runtime and ≈3-6× peak memory usage reduction for DNAm microarray imputation (GSE286313, EPICv2, N = 72) and achieved high imputation accuracy in a whole-genome DNAm dataset (N = 41). AVAILABILITY AND IMPLEMENTATION: The code used in this study is available at https://github.com/hhp94/slideimp_paper. The R package slideimp is available on CRAN (DOI: 10.32614/CRAN.package.slideimp). Version 1.0.0 of slideimp, which was used in this study, is archived on Zenodo (DOI: 10.5281/zenodo.20029382).