methylumi

Handle Illumina methylation data

Bioconductor version: Release (2.12)

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("methylumi")

Documentation

PDF	R Script	An Introduction to the methylumi package
PDF		Reference Manual
Text		README

Details

biocViews	CpGIsland, DNAMethylation, Preprocessing, QualityControl, Software, TwoChannel
Version	2.6.1
In Bioconductor since	BioC 2.5 (R-2.10)
License	GPL-2
Depends	Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2
Imports	Biobase, graphics, lattice, annotate, genefilter, AnnotationDbi, stats4, BiocGenerics, AnnotationForge, minfi
Suggests	lumi, lattice, limma, xtable, IlluminaHumanMethylation27k.db(>= 1.4.4), IlluminaHumanMethylation450k.db, SQN, GenomicRanges, MASS, matrixStats, parallel, rtracklayer, Biostrings, FDb.InfiniumMethylation.hg19
System Requirements
URL
Depends On Me	wateRmelon
Imports Me	ffpe, lumi, methyAnalysis
Suggests Me	IlluminaHumanMethylation450k.db

Package Downloads

Package Source	methylumi_2.6.1.tar.gz
Windows Binary	methylumi_2.6.1.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard)	methylumi_2.6.1.tgz
Package Downloads Report	Download Stats

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