metaX

Package: metaX
Type: Package
Title: An R package for metabolomic data analysis
Version: 1.4.2
Date: 2015-02-10
Author: Bo Wen <wenbo@genomics.cn>
Maintainer: Bo Wen <wenbo@genomics.cn>
Description: The package provides a integrated pipeline for mass spectrometry-
based metabolomic data analysis. It includes the stages peak detection, data
preprocessing, normalization, missing value imputation, univariate statistical
analysis, multivariate statistical analysis such as PCA and PLS-DA, metabolite
identification, pathway analysis, power analysis, feature selection and
modeling, data quality assessment.
Depends: R (>= 3.2.0), VennDiagram, pROC, SSPA, methods
Imports: Nozzle.R1, ggplot2, parallel, pcaMethods, reshape2, plyr,
BBmisc, mixOmics, preprocessCore, vsn, pls, impute, missForest,
doParallel, DiscriMiner, xcms, ape, scatterplot3d, pheatmap,
bootstrap, boot, caret, dplyr, stringr, RColorBrewer, DiffCorr,
RCurl, lattice, faahKO, data.table, CAMERA, igraph, tidyr,
scales
License: LGPL-2
URL: http://wenbostar.github.io/metaX/
BugReports: https://github.com/wenbostar/metaX/issues
Suggests: knitr, BiocStyle, R.utils, RUnit, BiocGenerics
VignetteBuilder: knitr
biocViews: Metabolomics, MassSpectrometry, QualityControl
RoxygenNote: 5.0.1
PackageStatus: Deprecated
NeedsCompilation: no
Packaged: 2016-05-16 05:38:16 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'metaX' ...
** R
** inst
** preparing package for lazy loading
in method for 'plotLoading' with signature 'object="mvr"': no definition for class "mvr"
** help
*** installing help indices
  converting help for package 'metaX'
    finding HTML links ... done
    addIdentInfo                            html  
    addValueNorm                            html  
    autoRemoveOutlier                       html  
    finding level-2 HTML links ... done

    bootPLSDA                               html  
    calcAUROC                               html  
    calcVIP                                 html  
    center                                  html  
    checkPvaluePlot                         html  
    checkQCPlot                             html  
    cor.network                             html  
    createModels                            html  
    dataClean                               html  
    dir.case                                html  
    dir.ctrl                                html  
    doQCRLSC                                html  
    featureSelection                        html  
    filterPeaks                             html  
    filterQCPeaks                           html  
    filterQCPeaksByCV                       html  
    getPeaksTable                           html  
    group.bw                                html  
    group.bw0                               html  
    group.max                               html  
    group.minfrac                           html  
    group.minsamp                           html  
    group.mzwid                             html  
    group.mzwid0                            html  
    group.sleep                             html  
    hasQC                                   html  
    idres                                   html  
    importDataFromMetaboAnalyst             html  
    importDataFromQI                        html  
    importDataFromXCMS                      html  
    kfold                                   html  
    makeDirectory                           html  
    makeMetaboAnalystInput                  html  
    metaXpara-class                         html  
    metaXpipe                               html  
    metaboliteAnnotation                    html  
    method                                  html  
    missValueImputeMethod                   html  
    missingValueImpute                      html  
    myCalcAUROC                             html  
    myPLSDA                                 html  
    ncomp                                   html  
    normalize                               html  
    nperm                                   html  
    outdir                                  html  
    pathwayAnalysis                         html  
    peakFinder                              html  
    peakStat                                html  
    peaksData                               html  
    permutePLSDA                            html  
    plotCV                                  html  
    plotCorHeatmap                          html  
    plotHeatMap                             html  
    plotIntDistr                            html  
    plotLoading                             html  
    plotMissValue                           html  
    plotNetwork                             html  
    plotPCA                                 html  
    plotPLSDA                               html  
    plotPeakBox                             html  
    plotPeakNumber                          html  
    plotPeakSN                              html  
    plotPeakSumDist                         html  
    plotQC                                  html  
    plotQCRLSC                              html  
    plotTreeMap                             html  
    plsDAPara-class                         html  
    powerAnalyst                            html  
    preProcess                              html  
    prefix                                  html  
    qcRlscSpan                              html  
    ratioPairs                              html  
    rawPeaks                                html  
    reSetPeaksData                          html  
    removeSample                            html  
    retcor.method                           html  
    retcor.plottype                         html  
    retcor.profStep                         html  
    runPLSDA                                html  
    sampleListFile                          html  
    scale                                   html  
    selectBestComponent                     html  
    t                                       html  
    transformation                          html  
    validation                              html  
    xcmsSet.fitgauss                        html  
    xcmsSet.fwhm                            html  
    xcmsSet.integrate                       html  
    xcmsSet.max                             html  
    xcmsSet.method                          html  
    xcmsSet.mzCenterFun                     html  
    xcmsSet.mzdiff                          html  
    xcmsSet.nSlaves                         html  
    xcmsSet.noise                           html  
    xcmsSet.peakwidth                       html  
    xcmsSet.polarity                        html  
    xcmsSet.ppm                             html  
    xcmsSet.prefilter                       html  
    xcmsSet.profparam                       html  
    xcmsSet.sleep                           html  
    xcmsSet.snthresh                        html  
    xcmsSet.step                            html  
    xcmsSet.verbose.columns                 html  
    xcmsSetObj                              html  
    zero2NA                                 html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: Package 'metaX' is deprecated and will be removed from Bioconductor
  version 3.3
* DONE (metaX)
Making 'packages.html' ... done