methylumi

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

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'methylumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'methylumi'
    finding HTML links ... done
    CpGs                                    html  
    MethyLumi-class                         html  
    finding level-2 HTML links ... done

    MethyLumiM-class                        html  
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:41: missing file link 'ExpressionSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:41: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:53: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:54: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:55: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:56: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:57: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:58: missing file link 'eSet-class'
Rd warning: /tmp/RtmpDBIper/R.INSTALL78b11e21341b/methylumi/man/MethyLumiM-class.Rd:70: missing file link 'eSet-class'
    MethyLumiQC-class                       html  
    MethyLumiSet-class                      html  
    estimateM                               html  
    extractBarcodeAndPosition               html  
    featureFilter                           html  
    generics                                html  
    getAssayDataNameSubstitutions           html  
    methylData-class                        html  
    methylumIDAT                            html  
    methylumi-package                       html  
    methylumiGenerics                       html  
    methylumiR                              html  
    mldat                                   html  
    normalizeMethyLumiSet                   html  
    plotSampleIntensities                   html  
    qcplot                                  html  
    stripBeadExtras                         html  
    varFilter                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (methylumi)
Making 'packages.html' ... done