geNetClassifier

Package: geNetClassifier
Type: Package
Title: Classify diseases and build associated gene networks using gene
expression profiles
Version: 1.12.0
Date: 2015-05-05
Author: Sara Aibar, Celia Fontanillo and Javier De Las Rivas.
Bioinformatics and Functional Genomics Group. Cancer Research
Center (CiC-IBMCC, CSIC/USAL). Salamanca. Spain.
Maintainer: Sara Aibar <saibar@usal.es>
Depends: R (>= 2.10.1), Biobase (>= 2.5.5), EBarrays, minet, methods
Imports: e1071, graphics
Suggests: leukemiasEset, RUnit, BiocGenerics
Enhances: RColorBrewer, igraph, infotheo
Description: Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.
License: GPL (>= 2)
ZipData: no
URL: http://www.cicancer.org
LazyLoad: yes
Collate: class.GenesRanking.R class.GenesNetwork.R
class.GeneralizationError.R class.GeNetClassifierReturn.R
functions.private.R functions.public.R function.main.R
biocViews: Classification, DifferentialExpression, Microarray
NeedsCompilation: no
Packaged: 2016-05-04 04:54:56 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'geNetClassifier' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'geNetClassifier'
    finding HTML links ... done
    GeNetClassifierReturn-class             html  
    GeneralizationError-class               html  
    GenesNetwork-class                      html  
    GenesRanking-class                      html  
    calculateGenesRanking                   html  
    externalValidation.probMatrix           html  
    externalValidation.stats                html  
    gClasses-methods                        html  
    geNetClassifier-package                 html  
    geNetClassifier                         html  
Rd warning: /tmp/Rtmp7HEtM5/R.INSTALLd1011497526/geNetClassifier/man/geNetClassifier.Rd:147: missing file link 'brewer.pal'
Rd warning: /tmp/Rtmp7HEtM5/R.INSTALLd1011497526/geNetClassifier/man/geNetClassifier.Rd:151: missing file link 'igraph'
    geneSymbols                             html  
    genesDetails-methods                    html  
    getEdges-methods                        html  
    getNodes-methods                        html  
    getNumEdges-methods                     html  
    getNumNodes-methods                     html  
    getRanking-methods                      html  
    getSubNetwork-methods                   html  
    getTopRanking-methods                   html  
    leukemiasClassifier                     html  
    network2txt                             html  
    numGenes-methods                        html  
    numSignificantGenes-methods             html  
    overview-methods                        html  
    plot.GeNetClassifierReturn              html  
    plot.GenesRanking                       html  
    plotAssignments                         html  
    plotDiscriminantPower                   html  
    plotExpressionProfiles                  html  
    plotNetwork                             html  
Rd warning: /tmp/Rtmp7HEtM5/R.INSTALLd1011497526/geNetClassifier/man/plotNetwork.Rd:74: missing file link 'igraph'
Rd warning: /tmp/Rtmp7HEtM5/R.INSTALLd1011497526/geNetClassifier/man/plotNetwork.Rd:84: missing file link 'igraph'
    queryGeNetClassifier                    html  
    querySummary                            html  
    setProperties-methods                   html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (geNetClassifier)
Making 'packages.html' ... done