ddgraph

Package: ddgraph
Imports: bnlearn (>= 2.8), gtools, pcalg, RColorBrewer, plotrix, MASS
Maintainer: Robert Stojnic <robert.stojnic@gmail.com>
License: GPL-3
Title: Distinguish direct and indirect interactions with Graphical
Modelling
LinkingTo: Rcpp
Type: Package
LazyLoad: yes
Author: Robert Stojnic
Description: Distinguish direct from indirect interactions in gene
regulation and infer combinatorial code from highly correlated
variables such as transcription factor binding profiles. The
package implements the Neighbourhood Consistent PC algorithm
(NCPC) and draws Direct Dependence Graphs to represent
dependence structure around a target variable. The package also
provides a unified interface to other Graphical Modelling
(Bayesian Network) packages for distinguishing direct and
indirect interactions.
Version: 1.16.0
Date: 2015-01-27
Depends: graph, methods, Rcpp
Suggests: Rgraphviz, e1071, ROCR, testthat
Collate: 'AllClassses.R' 'AllGenerics.R' 'calcDependence.R' 'citest.R'
'combinations.R' 'dsep.R' 'furlong.R' 'methods-CITestResult.R'
'methods-DDDataSet.R' 'methods-DDGraphEdge.R'
'methods-DDGraph.R' 'misc.R' 'ncpc.R' 'other-algorithms.R'
'plot-colour.R' 'plot.R' 'randomnet.R' 'resampling.R' 'svm.R'
biocViews: GraphAndNetwork
NeedsCompilation: yes
Packaged: 2016-05-04 04:31:38 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ddgraph' ...
** libs
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rcpp/include"   -fpic  -g -O2  -c mcX2cloop.cpp -o mcX2cloop.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ddgraph.so mcX2cloop.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ddgraph/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ddgraph'
    finding HTML links ... done
    CITestResult-dash-class                 html  
    CITestResultID                          html  
    CITestResultVar                         html  
    DDDataSet-dash-class                    html  
    DDGraph-dash-class                      html  
    DDGraphEdge-dash-class                  html  
    FurlongDataSet-dash-class               html  
    NCPCRobustness-dash-class               html  
    activePaths                             html  
    adjC-dot-allVarInx                      html  
    adjC-dot-allVarNames                    html  
    adjC-dot-condSetSize                    html  
    adjC-dot-targetInx                      html  
    adjC-dot-toIDs                          html  
    biased-dot-bn-dot-fit                   html  
    biased-dot-graph                        html  
    blockingNodes                           html  
    blockingVariables                       html  
    calcDependence                          html  
    calculateNCPCRobustnessStats            html  
    chisq-dot-val                           html  
    ciTest-comma-DDDataSet-dash-method      html  
    classLabels-comma-FurlongDataSet-dash-method
                                            html  
    color-dot-legend-dot-DDGraph            html  
    combinationsTest                        html  
    convertPvalueToColorIndex               html  
    convertToFactor                         html  
    customPlotPCAlgo                        html  
    dataType-comma-DDDataSet-dash-method    html  
    datasetName-comma-DDDataSet-dash-method
                                            html  
    ddgraph-package                         html  
    entropyFromFreq                         html  
    estimateNetworkDistribution             html  
    extract-dot-targetInx                   html  
    extractCITestResultProperty             html  
    foldChangeFromFreq                      html  
    formulaFalseNeg                         html  
    graph-dot-to-dot-bn                     html  
    independent-dot-contributions-dot-formula-dot-mul
                                            html  
    independent-dot-contributions-dot-formula
                                            html  
    initialize-comma-DDDataSet-dash-method
                                            html  
    initialize-comma-DDGraph-dash-method    html  
    is-dot-binary                           html  
    logseq                                  html  
    loocv                                   html  
    makeDDDataSet                           html  
    makeNCPCRobustness                      html  
    mapEnrichmentToColors                   html  
    mapEnrichmentToColorsDual               html  
    mcMITest                                html  
    mcX2CLoop                               html  
    mcX2Test                                html  
    mcX2TestB50k                            html  
    mesoBin                                 html  
    mesoCont                                html  
    myX2c                                   html  
    names-comma-CITestResult-dash-method    html  
    names-comma-DDDataSet-dash-method       html  
    names-comma-DDGraph-dash-method         html  
    names-comma-FurlongDataSet-dash-method
                                            html  
    ncpc                                    html  
    ncpcResampling                          html  
    operators-dash-CITestResult             html  
    operators-dash-DDDataSet                html  
    operators-dash-DDGraph                  html  
    pValueAfterMultipleTesting              html  
    pcalgMB                                 html  
    pcalgNBR                                html  
    plot-comma-DDGraph-comma-missing-dash-method
                                            html  
    plotBNLearn                             html  
    plotPCalg                               html  
    plotSVMPerformance                      html  
    predSVM                                 html  
    prob-dot-distr-dot-norm                 html  
    prob-dot-distr-dot-unif                 html  
    random-dot-bn-dot-fit                   html  
    rawData-comma-DDDataSet-dash-method     html  
    readFurlongData                         html  
    recalculateSVMparams                    html  
    show-comma-CITestResult-dash-method     html  
    show-comma-DDDataSet-dash-method        html  
    show-comma-DDGraph-dash-method          html  
    show-comma-DDGraphEdge-dash-method      html  
    signalMatrix-comma-FurlongDataSet-dash-method
                                            html  
    svmFeatureSelectionLOOCV                html  
    toDDDataSet-comma-FurlongDataSet-dash-method
                                            html  
    toyExample                              html  
    variableNames-comma-DDDataSet-dash-method
                                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ddgraph)
Making 'packages.html' ... done