Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
Biobase, methods, R (>= 2.13), scales, reshape2, ggplot2,
matrixStats, FDb.InfiniumMethylation.hg19 (>= 2.2.0), minfi
BiocGenerics, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges,
SummarizedExperiment, Biobase, graphics, lattice, annotate,
genefilter, AnnotationDbi, minfi, stats4, illuminaio
lumi, lattice, limma, xtable, SQN, MASS, matrixStats,
parallel, rtracklayer, Biostrings, methyAnalysis,
TCGAMethylation450k,
IlluminaHumanMethylation450kanno.ilmn12.hg19,
FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr
DNAMethylation, TwoChannel, Preprocessing, QualityControl,
CpGIsland
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.
AllGenerics.R MethyLumiSet-class.R MethyLumiM-class.R
MoreGenerics.R Methods.R bgcorr.R coercions.R detectionpval.R
featureFilter.R mclapply_replace.R methylData-class.R
methylumIDAT.R methylumiCSV.R methylumiR.R normalization.R
plotNegOob.R qc.probe.plot.R readIDAT2.R stripMethyLumiSet.R
utilities.R varFilter.R