# affylmGUI Menu Definitions

# last modified 09 10 2009 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    NGSMenu         topMenu         ""                                                              ""
    item    NGSMenu         command         "oneChannelGUI: miRNAs fq linker trimming"                                            adaptorTrimm
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu         command         "oneChannelGUI: Move to NGS menu to use tophat"                                            tuxedoMenu
    item    NGSMenu         command         "oneChannelGUI: New RNA-seq project"                                            NewLimmaFileNGS
    item    NGSMenu         command         "oneChannelGUI: Open    Ctrl+O"                                 OpenLimmaFile
    item    NGSMenu         command         "oneChannelGUI: Save As"                                        SaveAsLimmaFile
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "oneChannelGUI: Info about the loaded data set"                 showDataset
    item    NGSMenu        command         "oneChannelGUI: Export Normalized Expression Values"            ExportNormalizedExpressionValues1
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "affylmGUI: Working Directory"                                  SetWD
    item    NGSMenu        separator       ""                                                              ""
    item    NGSMenu        command         "affylmGUI: Exit"                                               onExit
    item    topMenu         cascade         "File (RNA-seq)"                                                          NGSMenu
   
    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 (Microarray)"                                          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: Controls Probes Raw Intensity Histogram"                 rawBoxplotPN
    item    plotMenu        command         "oneChannelGUI: Gene/Exon Intensity Histogram"                 ocPlotHist
    item    plotMenu        command         "oneChannelGUI: Gene/Exon PCA/HCL"                             ocPlotPCA
    item    plotMenu        separator       ""                                              ""
    item    plotMenu        command         "affylmGUI: Options"                                       PlotOptionsv1
    item    topMenu         cascade         "QC"                                       plotMenu

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


    menu    filteringMenu   topMenu         ""                                              ""
    item    filteringMenu   command         "oneChannelGUI: Setting to 0 log2 intensity below 1, to be used with plier only"       plierToZero
    item    filteringMenu   command         "oneChannelGUI: Filtering on DABG p-values"                dabgFilter
    item    filteringMenu   command         "oneChannelGUI: Set background threshold"       intronicBg
    item    filteringMenu   command         "oneChannelGUI: Filtering by background threshold intensity"            intensityFilter
    item    filteringMenu   command         "oneChannelGUI: Filtering by IQR"                  iqrFilter
#    item    filteringMenu   command         "oneChannelGUI: Filtering by reverse IQR (for alternative splicing analysis only!)"      reviqrFilter
    item    filteringMenu   separator       ""                                              ""
 #   item    filteringMenu   command         "oneChannelGUI: Filtering out cross hybridizing probe sets"                crosshybFilter
    item    filteringMenu   command         "oneChannelGUI: Selecting only probe sets with multiple mRNA association in ensembl"                biomartFilter
    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: Info about the loaded data set"                showDataset
    item    filteringMenu   separator       ""                                              ""
    item    filteringMenu   command         "oneChannelGUI: Recovering unfiltered data"                     recoverUnfiltered
    item    filteringMenu   command         "oneChannelGUI: Exporting Gene exprs and/or Exon/SI/MiDAS/RP data/elevel IDs to exon EGs"           ExportNormalizedExpressionValues1
    item    filteringMenu   command         "oneChannelGUI: Exporting Normalized Expression Values reformatted for meV software"           eSet4meV

    item    filteringMenu   command         "oneChannelGUI: Exporting Gene-level probe set ids"           ExportfeatureNames
    item    topMenu         cascade         "Filtering"                                filteringMenu


    menu    exonMenu        topMenu         ""                                              ""
 #  item    exonMenu        command         "oneChannelGUI: Correcting intensity signals using COSIE model"                                       cosieWrapper
    item    exonMenu        command         "oneChannelGUI: Calculating MiDAS p-value (APT)"                                AptMidas
    item    exonMenu        command         "oneChannelGUI: Calculating splice index"                                       spliceIndex
    item    exonMenu        command         "oneChannelGUI: Rank Product alternative splicing detection"            erankProdAltSpl
    item    exonMenu        separator         ""                                              ""
    item    exonMenu        command         "oneChannelGUI: Exon-level Linear Model Fit"                                limmaExons
    item    exonMenu        command         "oneChannelGUI: Compute Contrasts and regularised t-test p-values"          exonContrasts
    item    exonMenu        command         "oneChannelGUI: Limma alternative splicing detection"                   exonTopTableExtract
 
    item    exonMenu        separator       ""                                              ""
    item    exonMenu        command         "oneChannelGUI: Selecting alternative splicing events by MiDAS p-values"        midasFilter
    item    exonMenu       command         "oneChannelGUI: Selecting alternative splicing events by RankProd p-values"     erankProdAltSplFilter
    item    exonMenu       command         "oneChannelGUI: Filtering gene/exon data by absolute SI mean or min difference"     simFilter
    item    exonMenu        command         "oneChannelGUI: Selecting alternative splicing by RP/MiDAS p-values and mean/min delta SI"            consistentFilters
    item    exonMenu        separator       ""                                              ""
 #  item    exonMenu        command         "oneChannelGUI: Mapping exon level probe sets to EG exons"         mapping2ensembl
    item    exonMenu        command         "oneChannelGUI: Inspecting splice indexes"                                     inspecting.splice.index
    item    exonMenu        command         "oneChannelGUI: Inspecting splice indexes of one glevel probe set"             inspecting.one.splice.index
    item    exonMenu        command         "oneChannelGUI: Plotting a splicing event"             genomePlot
 #  item    exonMenu        command         "oneChannelGUI: Mapping exon level probe sets to Reference Sequences"         mapping2RefSeq
 #  item    exonMenu        command         "oneChannelGUI: Mapping exon level probe sets to the corresponding exon"         mapping2exon
    item    exonMenu        separator       ""                                              ""
    item    exonMenu        command         "oneChannelGUI: Exporting Gene-level probe set ids"           ExportfeatureNames
    item    exonMenu        command         "oneChannelGUI: Exporting Gene exprs and/or Exon/SI/MiDAS/RP data/elevel IDs to exon EGs"           ExportNormalizedExpressionValues1
    item    exonMenu        command         "oneChannelGUI: Recovering unfiltered data"                     recoverUnfiltered
    item    topMenu         cascade         "Exon analysis"                               exonMenu

    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: Two groups Linear Model with batch effect"             limma2paired        
    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 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    toptableMenu    topMenu         ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Attaching ACC and Entrez Gene IDs to Probe set IDs (EXON 1.0 ST)"                              EG2probeset
    item    toptableMenu    separator       ""                                                              ""
    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: Associating alternative spliced exon-level probe set to variant exons"          variantSI
    item    toptableMenu    command         "oneChannelGUI: Creating BED15 formatted files for visualization on UCSC browser"          makeBED15
    item    toptableMenu    command         "oneChannelGUI: Plot variant exons on UCSC browser"          plotVariantSI
    item    toptableMenu    separator       ""                                                              ""
#    item    toptableMenu    command         "oneChannelGUI: Mapping exon level probe sets to Reference Sequences"         mapping2RefSeq
    item    toptableMenu    command         "oneChannelGUI: Extracting exon-level PSR sequences associated to one gene-level probeset"         retrievePSRseq1gid
    item    toptableMenu    command         "oneChannelGUI: Exporting Gene exprs and/or Exon/SI/MiDAS/RP data/elevel IDs to exon EGs"           ExportNormalizedExpressionValues1
    item    toptableMenu    separator       ""                                                              ""
    item    toptableMenu    command         "oneChannelGUI: Starting meV clustering software"                      startmeV
    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    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    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    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: Installing all external software needed for RNA-seq"          wrapNGS
#    item    generalToolsMenu command         "oneChannelGUI: Install NGS perl scripts"          ngsperlDownload
    item    generalToolsMenu command         "oneChannelGUI: Set Java folder"          javaFolder
    item    generalToolsMenu command         "oneChannelGUI: Install Bowtie and Picard tools"          bowtieDownload
    item    generalToolsMenu command         "oneChannelGUI: Download and build hs, mm, rn bowtie reference sets (slow)"          bowtieGenomes
    item    generalToolsMenu command         "oneChannelGUI: Download built hs, mm, rn bowtie reference sets (fast)"          bowtieBuilt
    item    generalToolsMenu        separator       ""                                                              ""
    item    generalToolsMenu command         "oneChannelGUI: Set library folder, installing Affy gene/Exon libs and miRNAs refs for RNA-seq"          geneExonLibs
    item    generalToolsMenu command         "oneChannelGUI: Set Affymetrix apt tools folder"          aptFolder
    item    generalToolsMenu        separator       ""                                                              ""
    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: Reformat Genome Studio exported files"          genomeStudioReformat
    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         "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
