# oneChannelGUI Menu Definitions

# last modified 10 07 2007 RA Calogero 

# Based on Rcmdr-menus.txt from the Rcmdr package by John Fox, 

#   type    menu/item      operation/parent label                                                          command/menu
    
    menu    fileMenu        topMenu         ""                                                              ""
  # item    fileMenu        command        "oneChannelGUI: Create a Target file"                            targetWidget
    item    fileMenu        command         "oneChannelGUI: New     Ctrl+N"                                 NewLimmaFile
    item    fileMenu        command         "oneChannelGUI: Open    Ctrl+O"                                 OpenLimmaFile
 #  item    fileMenu        command         "affylmGUI: Save    Ctrl+S"                                     SaveLimmaFile
    item    fileMenu        command         "oneChannelGUI: Save As"                                        SaveAsLimmaFile
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "oneChannelGUI: Create a Target file from a GEO series matrix file" createGeoTarget
    item    fileMenu        command         "oneChannelGUI: Combining GEO matrix series files" combineGeoMSF
    item    fileMenu        separator       ""                                              ""
    item    fileMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    fileMenu        command         "oneChannelGUI: Export Normalized Expression Values"            ExportNormalizedExpressionValues1
#   item    fileMenu        command         "affylmGUI: Export TopTable (differentially expressed genes)"   ExportTopTable
#   item    fileMenu        command         "affylmGUI: Export HTML Report"                                 ExportHTMLreport
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "affylmGUI: Working Directory"                                  SetWD
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "affylmGUI: Exit"                                               onExit
    item    topMenu         cascade         "File"                                                          fileMenu

    menu    RNATargetsMenu  topMenu         ""                                                              ""
    item    RNATargetsMenu  command         "affylmGUI: View RNA Targets"                                   ViewRNATargets
    item    RNATargetsMenu  separator       ""                                                              ""
    item    RNATargetsMenu  command         "oneChannelGUI: maSigPro: Create/View edesign"                  masigpro.edesign
    item    RNATargetsMenu  command         "oneChannelGUI: Create/View classification parameters"          ML.edesign
    item    topMenu         cascade         "RNA Targets"                                                   RNATargetsMenu

    menu    plotMenu        topMenu         ""                                                              ""
    item    plotMenu        command         "affylmGUI: Intensity Histogram"                                IntensityHistogram
    item    plotMenu        command         "affylmGUI: Intensity Density Plot"                             DensityPlot
    item    plotMenu        command         "affylmGUI: Raw Intensity Box Plot"                             RawIntensityBoxPlot
    item    plotMenu        command         "affylmGUI: RNA Degradation Plot"                                          RNADegradationPlotAll
    item    plotMenu        command         "affylmGUI: M A Plot (for two slides)"                          affyPlotMA
    item    plotMenu        command         "affylmGUI: Image Array Plot(One slide)"                        ImageArrayPlot
    item    plotMenu        command         "affylmGUI: Normalized Intensity Box Plot"                      NormalizedIntensityBoxPlot
    item    plotMenu        separator       ""                                                              ""
    item    plotMenu        command         "affylmGUI: NUSE-Normalized Unscaled Std.Errors Plot"           NUSEPlotAll
    item    plotMenu        command         "affylmGUI: RLE-Relative Log Expression Plot"                   RLEPlotAll
    item    plotMenu        command         "affylmGUI: Weights pseudo chip Image(s) Plot"                  ImageQualityWeightPlot
    item    plotMenu        command         "affylmGUI: Residuals pseudo chip Image(s) Plot"                ImageQualityResidualPlot
    item    plotMenu        separator       ""                                                              ""
    item    plotMenu        command         "oneChannelGUI: Samples QC (PCA/HCL)"                               ocPlotPCA
    item    plotMenu        command         "oneChannelGUI: Box plot of normalized data"                               normBoxplot
    item    plotMenu        separator       ""                                                              ""
    item    plotMenu        command         "affylmGUI: Options"                                                       PlotOptionsv1
    item    topMenu         cascade         "QC"                                                            plotMenu

    menu    normalizeMenu   topMenu         ""                                                              ""
    item    normalizeMenu   command         "affylmGUI: probe set summary and normalization"                     NormalizeNow
    item    normalizeMenu   command         "oneChannelGUI: expresso (many options, but slow computing)"             myExpresso
    item    normalizeMenu   command         "oneChannelGUI: Info about the loaded data set"                          showDataset
    item    topMenu         cascade         "Probe set summary"                                             normalizeMenu

    menu    designMenu     topMenu          ""                                                              ""
#    item    designMenu     command          "oneChannelGUI: Sample size & statistical Power estimation (ssize pkg)"    sample.size.evaluation
    item    designMenu     command          "oneChannelGUI: Sample size & statistical Power estimation ((sizepower pkg)"    sample.size.evaluation1
    item    topMenu        cascade          "Study design"                                                  designMenu

    menu    filteringMenu   topMenu         ""                                                              ""
    item    filteringMenu   command         "oneChannelGUI: Filtering by IQR"                              iqrFilter
    item    filteringMenu   command         "oneChannelGUI: Filtering by intensity"                        intensityFilter
    item    filteringMenu   separator       ""                                                              ""
    item    filteringMenu   command         "oneChannelGUI: Filtering using a list of probe sets"                          listFilter
    item    filteringMenu   command         "oneChannelGUI: Filtering using a list of Entrez Genes"                        IPAlistFilter
    item    filteringMenu   separator       ""                                                              "" 
    item    filteringMenu   command         "oneChannelGUI: Recovering unfiltered data"                     recoverUnfiltered
    item    filteringMenu   command         "oneChannelGUI: Export Normalized Expression Values"            ExportNormalizedExpressionValues1
    item    filteringMenu   command         "oneChannelGUI: Exporting Gene-level probe set ids"           ExportfeatureNames
    item    topMenu         cascade         "Filtering"                                                     filteringMenu

    menu    linearModelMenu topMenu         ""                                                              ""
    item    linearModelMenu command         "affylmGUI: Compute Linear Model Fit"                           ComputeLinearModelFit
    item    linearModelMenu command         "affylmGUI: Compute Contrasts"                                  ComputeContrasts
    item    linearModelMenu command         "oneChannelGUI: Raw p-value distribution plot"                  rawpCheck
    item    linearModelMenu command         "affylmGUI: View Existing Contrasts Parameterization"           ViewExistingContrastParameterization
    item    linearModelMenu command         "affylmGUI: Delete Contrasts Parameterization"                  DeleteContrastParameterization 
    item    linearModelMenu command         "oneChannelGUI: Table of Genes Ranked in order of Differential Expression"   showTopTable
    item    linearModelMenu separator       ""                                                              ""
    item    linearModelMenu command         "affylmGUI: Quantile-Quantile t Statistic Plot (for one contrast)"  QQTplot

    item    linearModelMenu command         "oneChannelGUI: Venn Diagram between probe set lists"           VennDiagram
    item    linearModelMenu separator       ""                                                              ""
    item    linearModelMenu separator       ""                                                              ""
    item    linearModelMenu command         "oneChannelGUI: Create an edesign for maSigPro"                 masigpro.edesign
    item    linearModelMenu command         "oneChannelGUI: Execute maSigPro"                               masigpro
    item    linearModelMenu command         "oneChannelGUI: View maSigPro results"                          masigpro.view
    item    linearModelMenu separator       ""                                                              ""
    item    topMenu         cascade         "Modeling statistics"                                          linearModelMenu

    menu    siggenesMenu    topMenu         ""                                                              ""
    item    siggenesMenu    command         "oneChannelGUI: SAM analysis"                                   siggenes
    item    siggenesMenu    command         "oneChannelGUI: Rank product analysis"                          rankProd
    item    topMenu         cascade         "Permutation statistics"                                        siggenesMenu

    menu    classificationMenu    topMenu         ""                                                        ""
    item    classificationMenu  command         "oneChannelGUI: Create/View classification parameters"      ML.edesign
    item    classificationMenu  command         "oneChannelGUI: Reset classification parameters"            delete.ML
    item    classificationMenu    command       "oneChannelGUI: Create a training/test set"                 trainTest
    item    topMenu         cascade         "Classification"                                                classificationMenu

    menu    toptableMenu    topMenu         ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Identifying enriched GO terms"                              GOenrichment
    item    toptableMenu    command         "oneChannelGUI: Plotting the parents of a GO term"                    plotGO
    item    toptableMenu    command         "oneChannelGUI: Extracting Affy IDs linked to an enriched GO term"    extractAffyids
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Making template A for Ingenuity analysis"                      templA
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Merging the same set of probe sets from different data sets (devel)"     metaArrayMerge
    item    toptableMenu    command         "oneChannelGUI: Mining similarities/dissimilarities between merged data sets (IC) (devel)"   metaArrayIC
    item    topMenu         cascade         "Biological Interpretation"                                                       toptableMenu

    menu    generalToolsMenu  topMenu         ""                                                            ""
    item    generalToolsMenu  command       "oneChannelGUI: Filtering a tab delimited file"                 filteringTable
    item    generalToolsMenu  command       "oneChannelGUI: Extract a column from a tab delimited file"                                colExtract
    item    generalToolsMenu command         "oneChannelGUI: Venn Diagram between probe set lists"          VennDiagram
    item    generalToolsMenu        separator       ""                                                              ""
    item    generalToolsMenu command         "oneChannelGUI: Set library folder and install Affy gene/Exon library files"          geneExonLibs
    item    generalToolsMenu command         "oneChannelGUI: Set Affymetrix apt tools folder"          aptFolder
    item    generalToolsMenu command         "oneChannelGUI: Update all Bioconductor Libraries"          updateLibs
    item    generalToolsMenu command         "oneChannelGUI: Update gene-level annotation via Netaffx"          buildingLocalAnnotation
    item    generalToolsMenu command         "oneChannelGUI: Retrieve Reference Sequences fasta file from NCBI"          refseqDownload
    item    generalToolsMenu command         "oneChannelGUI: Reset Local Data info"          deleteLocalData
    item    generalToolsMenu    command         "affylmGUI: Evaluate R Code"                                evalRcode
    item    topMenu         cascade         "General Tools"                                                 generalToolsMenu
 
    menu    helpMenu        topMenu         ""                                                              ""
    item    helpMenu        command         "oneChannelGUI Help"                                            oneChannelGUIHelp
    item    helpMenu        command         "affylmGUI: affylmGUI Help"                                     affylmGUIhelp
    item    helpMenu        command         "affylmGUI: affy Help"                                          affyHelp
    item    helpMenu        command         "oneChannelGUI: AffyPLM Help"                                   affyPLMHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "oneChannelGUI: ssize Help"                                     ssizeHelp
    item    helpMenu        command         "oneChannelGUI: sizepower Help"                                 sizepowerHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "oneChannelGUI: genefilter Help"                                genefilterHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "affylmGUI: limma Help"                                         limmaHelp
    item    helpMenu        command         "oneChannelGUI: siggenes Help"                                  siggenesHelp
    item    helpMenu        command         "oneChannelGUI: maSigPro Help"                                  maSigProHelp
    item    helpMenu        command         "oneChannelGUI: RankProd Help"                                  RankProdHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "oneChannelGUI: GOstats Help"                                   GOstatsHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "oneChannelGUI: pdmclass Help"                                  pdmclassHelp
    item    helpMenu        command         "oneChannelGUI: pamr Help"                                      pamrHelp
    item    helpMenu        separator       ""                                                              ""
    item    helpMenu        command         "affylmGUI: About affylmGUI"                                    AboutaffylmGUI
    item    helpMenu        command         "oneChannelGUI: About oneChannelGUI"                            AboutextendedaffylmGUI
    item    helpMenu        command         "affylmGUI: Citations"                                          showCitations
    item    topMenu         cascade         "Help"                                                          helpMenu
