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Handle Illumina methylation data

Bioconductor version: Release (3.19)

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla

Maintainer: Sean Davis <seandavi at>

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


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:

An Introduction to the methylumi package PDF R Script
Working with Illumina 450k Arrays using methylumi PDF R Script
Reference Manual PDF


biocViews CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 2.50.0
In Bioconductor since BioC 2.5 (R-2.10) (14.5 years)
License GPL-2
Depends Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2, matrixStats, FDb.InfiniumMethylation.hg19(>= 2.2.0), minfi
Imports BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio, GenomicFeatures
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Suggests lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, knitr
Linking To
Depends On Me bigmelon, RnBeads, skewr, wateRmelon
Imports Me ffpe, lumi, missMethyl
Suggests Me
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package methylumi_2.50.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) methylumi_2.50.0.tgz
macOS Binary (arm64) methylumi_2.50.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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