MineICA

Package: MineICA
Type: Package
Title: Analysis of an ICA decomposition obtained on genomics data
Version: 1.12.0
Date: 2012-03-16
Author: Anne Biton
Maintainer: Anne Biton <anne.biton@gmail.com>
Description: The goal of MineICA is to perform Independent Component
Analysis (ICA) on multiple transcriptome datasets, integrating
additional data (e.g molecular, clinical and pathological).
This Integrative ICA helps the biological interpretation of the
components by studying their association with variables (e.g
sample annotations) and gene sets, and enables the comparison
of components from different datasets using correlation-based
graph.
License: GPL-2
LazyLoad: yes
Depends: R (>= 2.10), methods, BiocGenerics (>= 0.13.8), Biobase, plyr,
ggplot2, scales, foreach, xtable, biomaRt, gtools, GOstats,
cluster, marray, mclust, RColorBrewer, colorspace, igraph,
Rgraphviz, graph, annotate, Hmisc, fastICA, JADE
Imports: AnnotationDbi, lumi, fpc, lumiHumanAll.db
Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph,
breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP,
breastCancerVDX
Enhances: doMC
Collate: 'AllClasses.R' 'AllGeneric.R' 'methods-IcaSet.R'
'methods-MineICAParams.R' 'compareAnalysis.R'
'functions_comp2annot.R' 'functions_comp2annottests.R'
'functions_enrich.R' 'functions.R' 'heatmap.plus.R'
'heatmapsOnSel.R' 'runAn.R' 'compareGenes.R'
biocViews: Visualization, MultipleComparison
NeedsCompilation: no
Packaged: 2016-05-05 03:47:04 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'MineICA' ...
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'sampleNames<-' in package 'MineICA'
** help
*** installing help indices
  converting help for package 'MineICA'
    finding HTML links ... done
    A                                       html  
    Alist                                   html  
    Slist                                   html  
    addGenesToGoReport                      html  
    annot2Color                             html  
    annotCarbayo                            html  
    annotFeatures                           html  
    annotFeaturesComp                       html  
    annotFeaturesWithBiomaRt                html  
    annotInGene                             html  
    annotReciprocal                         html  
    buildIcaSet                             html  
    buildMineICAParams                      html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/buildMineICAParams.Rd:50: missing file link 'MineICAParams-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/buildMineICAParams.Rd:54: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/buildMineICAParams.Rd:67: missing file link 'MineICAParams-class'
    build_sortHeatmap                       html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/build_sortHeatmap.Rd:45: missing file link 'IcaSet-class'
    class-IcaSet                            html  
    finding level-2 HTML links ... done

    class-MineICAParams                     html  
    clusVarAnalysis                         html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/clusVarAnalysis.Rd:16: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/clusVarAnalysis.Rd:19: missing file link 'MineICAParams-class'
    clusterFastICARuns                      html  
    clusterSamplesByComp                    html  
    clusterSamplesByComp_multiple           html  
    compareAn                               html  
    compareAn2graphfile                     html  
    compareGenes                            html  
    cor2An                                  html  
    correl2Comp                             html  
    dat                                     html  
    dataCarbayo                             html  
    doEnrichment                            html  
    getComp                                 html  
    getProj                                 html  
    getSdExpr                               html  
    hgOver                                  html  
    hypergeoAn                              html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/hypergeoAn.Rd:53: missing file link 'GOstats'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/hypergeoAn.Rd:14: missing file link 'MineICAParams-class'
    icaSetCarbayo                           html  
    icaSetKim                               html  
    icaSetRiester                           html  
    icaSetStransky                          html  
    indComp                                 html  
    mergeGostatsResults                     html  
    nbOccByGeneInComp                       html  
    nbOccInComp                             html  
    nbOccInComp_simple                      html  
    nodeAttrs                               html  
    plotAllMix                              html  
    plotCorGraph                            html  
    plotDens2classInComp_plotOnly           html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotDens2classInComp_plotOnly.Rd:3: missing link 'ggplot2'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotDens2classInComp_plotOnly.Rd:82: missing link 'ggplot2'
    plotDensAllAnnotInAllComp               html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotDensAllAnnotInAllComp.Rd:14: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotDensAllAnnotInAllComp.Rd:17: missing file link 'MineICAParams-class'
    plotDensOneAnnotInAllComp               html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotDensOneAnnotInAllComp.Rd:12: missing file link 'IcaSet-class'
    plotMclust                              html  
    plotMix                                 html  
    plotPosAnnotInComp                      html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosAnnotInComp.Rd:80: missing file link 'IcaSet-class'
    plotPosOneAnnotInComp_ggplot            html  
    plotPosOneAnnotLevInComp_ggplot         html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosOneAnnotLevInComp_ggplot.Rd:3: missing link 'ggplot2'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosOneAnnotLevInComp_ggplot.Rd:54: missing link 'ggplot2'
    plotPosSamplesInComp                    html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosSamplesInComp.Rd:60: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosSamplesInComp.Rd:22: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/plotPosSamplesInComp.Rd:101: missing file link 'IcaSet-class'
    plot_heatmapsOnSel                      html  
    qualVarAnalysis                         html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/qualVarAnalysis.Rd:17: missing file link 'MineICAParams-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/qualVarAnalysis.Rd:21: missing file link 'IcaSet-class'
    quantVarAnalysis                        html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/quantVarAnalysis.Rd:17: missing file link 'MineICAParams-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/quantVarAnalysis.Rd:21: missing file link 'IcaSet-class'
    readA                                   html  
    readS                                   html  
    relativePath                            html  
    runAn                                   html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/runAn.Rd:22: missing file link 'MineICAParams-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/runAn.Rd:26: missing file link 'IcaSet-class'
    runCompareIcaSets                       html  
    runEnrich                               html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/runEnrich.Rd:11: missing file link 'IcaSet-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/runEnrich.Rd:14: missing file link 'MineICAParams-class'
    runICA                                  html  
    selectContrib                           html  
    selectFeatures_IQR                      html  
    selectWitnessGenes                      html  
    wilcoxOrKruskalOnA                      html  
    writeGenes                              html  
    writeGostatsHtmltable                   html  
    writeHtmlResTestsByAnnot                html  
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/writeHtmlResTestsByAnnot.Rd:14: missing file link 'MineICAParams-class'
Rd warning: /tmp/Rtmp4uhaaH/R.INSTALL59915f42c4d/MineICA/man/writeHtmlResTestsByAnnot.Rd:18: missing file link 'IcaSet-class'
    writeProjByComp                         html  
    writeRnkFiles                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (MineICA)
Making 'packages.html' ... done