# 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         "oneChannelGUI: Reformat NGS primary mapping output"                 NGSreformat
    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    normalizeMenu   command         "oneChannelGUI: Scale/normalize NGS data"                          edgeRNorm
    item    normalizeMenu   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: Multidimensional scaling plot (edgeR package)"                               qcMDS
    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: Filtering by counts threshold"            intensityFilter
    item    filteringMenu   command         "oneChannelGUI: Filtering using a list of probe sets"          listFilter
    item    filteringMenu   command         "oneChannelGUI: Recovering unfiltered data"                     recoverUnfiltered
    item    filteringMenu   separator       ""                                              ""
    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    filteringMenu   command         "oneChannelGUI: Exporting counts Values reformatted for meV software"           eSet4meV
    item    topMenu         cascade         "Filtering"                                                     filteringMenu

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

    menu    toptableMenu    topMenu         ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Adding annotation to NGS data set"                              annotateNGSeset
    item    toptableMenu    command         "oneChannelGUI: Starting meV clustering software"                      startmeV
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Detecting miR targets via RmiR package"                      RmiRInterface
    item    toptableMenu    command         "oneChannelGUI: Extract miR targets from RmiR output"                      extractmirTargets
    item    toptableMenu    command         "oneChannelGUI: Retrieve miR targets from RmiR.Hs.miRNA"                      retrieveMirTargets
    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 NGS perl scripts folder"          ngsperlDownload
    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: Installing meV clustering software"                              meVDownload
    item    generalToolsMenu    command         "oneChannelGUI: Information on external software and data connected to oneChannelGUI"                              extPckInfo
    item    generalToolsMenu        separator       ""                                                              ""
#    item    generalToolsMenu command         "oneChannelGUI: Update all Bioconductor Libraries"          updateLibs
    item    generalToolsMenu command         "oneChannelGUI: Update gene-level annotation via Netaffx"          buildingLocalAnnotation
     item    generalToolsMenu command         "oneChannelGUI: Update The UCSC tables linking exon-level probsets to variant exons"          variantExons
    item    generalToolsMenu command         "oneChannelGUI: Retrieve Reference Sequences fasta file from NCBI"          refseqDownload
    item    generalToolsMenu command         "oneChannelGUI: Reset Local Data info"          deleteLocalData
    item    generalToolsMenu    command         "oneChannelGUI: Export non-coding RNA fasta reference file for ncRNA-seq quantitative analysis"                              exportFASTA
    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         "oneChannelGUI: About oneChannelGUI"                            AboutextendedaffylmGUI
    item    helpMenu        command         "affylmGUI: Citations"                                          showCitations
    item    topMenu         cascade         "Help"                                                          helpMenu
