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Package: methylumi
Type: Package
Title: Handle Illumina methylation data
Version: 2.18.2
Date: 2015-06-30
Author: Sean Davis, Pan Du, Sven Bilke, Tim Triche, Jr., Moiz Bootwalla
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
biocViews: DNAMethylation, TwoChannel, Preprocessing, QualityControl,
CpGIsland
Maintainer: Sean Davis <sdavis2@mail.nih.gov>
Description: 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.
Collate: 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
VignetteBuilder: knitr
BugReports: https://github.com/seandavi/methylumi/issues/new
License: GPL-2
NeedsCompilation: no
Packaged: 2016-05-16 02:06:25 UTC; biocbuild
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providing 
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