# affylmGUI Menu Definitions

# last modified 30 12 2006 RA Calogero bis
#lodading this menu in changeMenu.R

# 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: 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: Attaching annotation library info"             addAnnLib
    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         "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         "oneChannelGUI: Normalization methods for raw data loaded as tab delimited files"        largedatasetNorm
    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 ((sizepwer 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: Info about the loaded data set"                showDataset
    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         "oneChannelGUI: Venn Diagram between probe set lists"          VennDiagram
    item    linearModelMenu command         "affylmGUI: Quantile-Quantile t Statistic Plot (for one contrast)"  QQTplot
    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    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: 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
