DOI: 10.18129/B9.bioc.methylumi    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see methylumi.

Handle Illumina methylation data

Bioconductor version: 3.7

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 <sdavis2 at>

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


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


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 2.26.0
In Bioconductor since BioC 2.5 (R-2.10) (9 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
Suggests lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18(>= 2.2.0), Homo.sapiens, knitr
Depends On Me bigmelon, RnBeads, skewr, wateRmelon
Imports Me ffpe, lumi, methyAnalysis, missMethyl
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package methylumi_2.26.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) methylumi_2.26.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Package Short Url
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: