lumi

Package: lumi
Type: Package
Title: BeadArray Specific Methods for Illumina Methylation and
Expression Microarrays
Version: 2.24.0
Date: 2015-07-02
Depends: R (>= 2.10), Biobase (>= 2.5.5)
Imports: affy (>= 1.23.4), methylumi (>= 2.3.2), GenomicFeatures,
GenomicRanges, annotate, Biobase (>= 2.5.5), lattice, mgcv (>=
1.4-0), nleqslv, KernSmooth, preprocessCore, RSQLite, DBI,
AnnotationDbi, MASS, graphics, stats, stats4, methods
Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db,
lumiHumanIDMapping, genefilter, RColorBrewer
Author: Pan Du, Richard Bourgon, Gang Feng, Simon Lin
Maintainer: Pan Du <dupan.mail@gmail.com>
Description: The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
License: LGPL (>= 2)
LazyLoad: yes
biocViews: Microarray, OneChannel, Preprocessing, DNAMethylation,
QualityControl, TwoChannel
NeedsCompilation: no
Packaged: 2016-05-04 02:59:12 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'lumi' ...
** R
** data
** inst
** preparing package for lazy loading
** help
Warning: bad markup (extra space?) at lumiMethyR.Rd:18:16
Warning: bad markup (extra space?) at lumiMethyR.Rd:19:28
Warning: bad markup (extra space?) at lumiMethyR.Rd:20:13
*** installing help indices
  converting help for package 'lumi'
    finding HTML links ... done
    IlluminaID2nuID                         html  
    LumiBatch-class                         html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:44: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:46: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:83: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:84: missing file link 'eSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:85: missing file link 'eSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:86: missing file link 'eSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:103: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:104: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:104: missing file link 'eSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:106: missing file link 'eSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:113: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/LumiBatch-class.Rd:113: missing file link 'eSet'
    MAplot-methods                          html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/MAplot-methods.Rd:16: missing file link 'ExpressionSet'
    addAnnotationInfo                       html  
    addControlData2lumi                     html  
    addControlData2methyLumiM               html  
    addNuID2lumi                            html  
    adjColorBias.quantile                   html  
    adjColorBias.ssn                        html  
    asBigMatrix-methods                     html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/asBigMatrix-methods.Rd:15: missing file link 'ExpressionSet'
    beta2m                                  html  
    bgAdjust                                html  
    bgAdjustMethylation                     html  
    boxplot-MethyLumiM-methods              html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/boxplot-MethyLumiM-methods.Rd:6: missing file link 'hdr.boxplot'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/boxplot-MethyLumiM-methods.Rd:16: missing file link 'bwplot'
    boxplot-methods                         html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/boxplot-methods.Rd:15: missing file link 'ExpressionSet'
    boxplotColorBias                        html  
    colorBiasSummary                        html  
    density-methods                         html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/density-methods.Rd:17: missing file link 'ExpressionSet'
    detectOutlier                           html  
    detectionCall                           html  
    estimateBeta                            html  
    estimateIntensity                       html  
    estimateLumiCV                          html  
    estimateM                               html  
    estimateMethylationBG                   html  
    example.lumi                            html  
    example.lumiMethy                       html  
    example.methyTitration                  html  
    gammaFitEM                              html  
    getChipInfo                             html  
    getChrInfo                              html  
    getControlData                          html  
    getControlProbe                         html  
    getControlType                          html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/getControlType.Rd:20: missing file link 'controlTypes'
    getNuIDMappingInfo                      html  
    hist-methods                            html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/hist-methods.Rd:15: missing file link 'ExpressionSet'
    id2seq                                  html  
    importMethyIDAT                         html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/importMethyIDAT.Rd:7: missing file link 'lumIDAT'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/importMethyIDAT.Rd:20: missing file link 'lumIDAT'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/importMethyIDAT.Rd:23: missing file link 'lumIDAT'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/importMethyIDAT.Rd:37: missing file link 'lumIDAT'
    inverseVST                              html  
    is.nuID                                 html  
    lumi.package                            html  
    lumiB                                   html  
    lumiExpresso                            html  
    lumiMethyB                              html  
    lumiMethyC                              html  
    lumiMethyN                              html  
    lumiMethyR                              html  
    lumiMethyStatus                         html  
    lumiN                                   html  
    lumiQ                                   html  
    lumiR                                   html  
    lumiR.batch                             html  
    lumiT                                   html  
    m2beta                                  html  
    methylationCall                         html  
    monoSmu                                 html  
    monoSpline                              html  
    normalizeMethylation.quantile           html  
    normalizeMethylation.ssn                html  
    nuID2EntrezID                           html  
    nuID2IlluminaID                         html  
    nuID2RefSeqID                           html  
    nuID2probeID                            html  
    nuID2targetID                           html  
    pairs-methods                           html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/pairs-methods.Rd:16: missing file link 'ExpressionSet'
    plot-methods                            html  
    plotCDF                                 html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/plotCDF.Rd:17: missing file link 'ExpressionSet'
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/plotCDF.Rd:29: missing file link 'plot.ecdf'
    plotColorBias1D                         html  
    plotColorBias2D                         html  
    plotControlData                         html  
    plotDensity                             html  
Rd warning: /tmp/RtmpE10MVb/R.INSTALL78d6745b8d39/lumi/man/plotDensity.Rd:14: missing file link 'ExpressionSet'
    plotGammaFit                            html  
    plotHousekeepingGene                    html  
    plotSampleRelation                      html  
    plotStringencyGene                      html  
    plotVST                                 html  
    probeID2nuID                            html  
    produceGEOPlatformFile                  html  
    produceGEOSampleInfoTemplate            html  
    produceGEOSubmissionFile                html  
    produceMethylationGEOSubmissionFile     html  
    rankinvariant                           html  
    rsn                                     html  
    seq2id                                  html  
    smoothQuantileNormalization             html  
    ssn                                     html  
    targetID2nuID                           html  
    vst                                     html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (lumi)
Making 'packages.html' ... done