# 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: New     Ctrl+N"                                 NewLimmaFile
    item    fileMenu        command         "oneChannelGUI: Open    Ctrl+O"                                 OpenLimmaFile
    item    fileMenu        command         "oneChannelGUI: Save As"                                        SaveAsLimmaFile
    item    fileMenu        separator       ""                                                              ""
    item    fileMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    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    topMenu         cascade         "RNA Targets"                                                   RNATargetsMenu


    menu    normalizeMenu   topMenu         ""                                                              ""
    item    normalizeMenu   command         "oneChannelGUI: Refining peaks"                          refiningPeaks
    item    normalizeMenu   command         "oneChannelGUI: Log2 transformation of reads counts"                          log2Conversion
    item    fileMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    topMenu         cascade         "Refining NGS peaks"                                             normalizeMenu

    menu    plotMenu        topMenu         ""                                              ""
    item    plotMenu        command         "oneChannelGUI: Samples QC (PCA/HCL)"                               ocPlotPCA
    item    plotMenu        command         "oneChannelGUI: Box plot of peaks counts"                               normBoxplot
    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "affylmGUI: Options"                                       PlotOptionsv1
    item    topMenu         cascade         "QC"                                       plotMenu


    menu    filteringMenu   topMenu         ""                                                              ""
    item    filteringMenu   command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    filteringMenu   command         "oneChannelGUI: Export counts Values"                          ExportNormalizedExpressionValues1
    item    filteringMenu   command         "oneChannelGUI: Exporting peaks ids"            ExportfeatureNames
    item    topMenu         cascade         "Filtering"                                                     filteringMenu

    menu    statsMenu topMenu         ""                                                              ""
    item    statsMenu    command         "oneChannelGUI: edgeR"                          edgerInterface
    item    statsMenu    command         "oneChannelGUI: Rank product analysis"                          rankProd
    item    topMenu         cascade         "Statistics"                                                    statsMenu

    menu    toptableMenu    topMenu         ""                                                              ""
    item    topMenu         cascade         "Biological Interpretation"                                                       toptableMenu

    menu    generalToolsMenu  topMenu         ""                                                            ""
    item    generalToolsMenu    command         "oneChannelGUI: Adding annotation to NGS data set"                              annotateNGSeset
    item    generalToolsMenu    command         "oneChannelGUI: Export non-coding RNA fasta reference file for ncRNA-seq quantitative analysis"                              exportFASTA
    item    topMenu         cascade         "General Tools"                                                 generalToolsMenu
 
    menu    helpMenu        topMenu         ""                                                              ""
    item    helpMenu        command         "oneChannelGUI Help"                                            oneChannelGUIHelp
    item    helpMenu        command         "oneChannelGUI: About oneChannelGUI"                            AboutextendedaffylmGUI
    item    helpMenu        command         "affylmGUI: Citations"                                          showCitations
    item    topMenu         cascade         "Help"                                                          helpMenu
