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Missing value estimation of DNA methylation data

Bioconductor version: Release (3.19)

This package allows to estimate missing values in DNA methylation data. methyLImp method is based on linear regression since methylation levels show a high degree of inter-sample correlation. Implementation is parallelised over chromosomes since probes on different chromosomes are usually independent. Mini-batch approach to reduce the runtime in case of large number of samples is available.

Author: Pietro Di Lena [aut] , Anna Plaksienko [aut, cre] , Claudia Angelini [aut] , Christine Nardini [aut]

Maintainer: Anna Plaksienko <anna at>

Citation (from within R, enter citation("methyLImp2")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

methyLImp2 vignette HTML R Script
Reference Manual PDF


biocViews DNAMethylation, MethylationArray, Microarray, Regression, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License GPL-3
Depends R (>= 4.3.0), ChAMPdata
Imports BiocParallel, parallel, stats, methods, corpcor, SummarizedExperiment, utils
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Follow Installation instructions to use this package in your R session.

Source Package methyLImp2_1.0.0.tar.gz
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macOS Binary (x86_64) methyLImp2_1.0.0.tgz
macOS Binary (arm64) methyLImp2_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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