DOI: 10.18129/B9.bioc.methylumi  

This is the development version of methylumi; for the stable release version, see methylumi.

Handle Illumina methylation data

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel


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:



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


biocViews CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 2.47.0
In Bioconductor since BioC 2.5 (R-2.10) (14 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
Suggests lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, knitr
Depends On Me bigmelon, RnBeads, skewr, wateRmelon
Imports Me ffpe, lumi, missMethyl
Suggests Me
Links To Me
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Source Package methylumi_2.47.0.tar.gz
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macOS Binary (arm64) methylumi_2.47.0.tgz
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