To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("methylumi")

In most cases, you don't need to download the package archive at all.

methylumi

 

Handle Illumina methylation data

Bioconductor version: Release (3.1)

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 mail.nih.gov>

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

Installation

To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("methylumi")

Documentation

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

browseVignettes("methylumi")

 

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

Details

biocViews CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version 2.14.0
In Bioconductor since BioC 2.5 (R-2.10) (5.5 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, Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, minfi, stats4, illuminaio
LinkingTo
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
SystemRequirements
Enhances
URL
BugReports https://github.com/seandavi/methylumi/issues/new
Depends On Me RnBeads, skewr, wateRmelon
Imports Me ffpe, lumi, methyAnalysis, missMethyl
Suggests Me IlluminaHumanMethylation450k.db
Build Report  

Package Archives

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

Package Source methylumi_2.14.0.tar.gz
Windows Binary methylumi_2.14.0.zip
Mac OS X 10.6 (Snow Leopard) methylumi_2.14.0.tgz
Mac OS X 10.9 (Mavericks) methylumi_2.14.0.tgz
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