limmaGUI              package:limmaGUI              R Documentation

_G_r_a_p_h_i_c_a_l _U_s_e_r _I_n_t_e_r_f_a_c_e _f_o_r _t_h_e _l_i_m_m_a _m_i_c_r_o_a_r_r_a_y _p_a_c_k_a_g_e

_D_e_s_c_r_i_p_t_i_o_n:

     Graphical User Interface for the limma microarray package

_U_s_a_g_e:

     AboutLimmaGUI()
     AboutNormalization()
     BChelp()
     ChooseContrastsParameterization(parameterizationTreeIndex)
     ChooseEbayesStatistic()
     ChooseParameterization()
     ChoosePlotSymbolByClicking(spotType, cex)
     ChooseSpotType(parameterizationTreeIndex)
     ComputeContrasts()
     CopyGraph(img)
     CreateNewParameterization()
     DeleteContrastsParameterization()
     deleteItemFromList(list1, itemName = NULL, index = NULL)
     DeleteParameterization()
     DupCorBoxPlot()
     ebayesBoxPlots()
     evalRcode()
     ExportHTMLreport()
     ExportTopTable()
     fixSeps(string)
     GetBackgroundCorrectionMethod()
     GetBetweenArrayNormalizationMethod()
     GetCoef(parameterizationTreeIndex, whichCoef = "onlyOne")
     GetComponentsToExportInHTMLreport(parameterizationIndex = NULL)
     GetContrastsParameterizationName()
     GetContrastsParameterizationNames(parameterizationTreeIndex)
     GetDEcutoff()
     GetDesignOrContrasts(Design = FALSE, Contrasts = FALSE, NumContrasts = 0,parameterizationIndex = 0)
     GetGeneLabelsOptions()
     GetImageAnalysisColumnHeadings()
     GetImageProcessingFileType()
     GetJpegOrPngParams(graphFileType)
     GetJpegOrPngX11Params(graphFileType)
     GetlimmaDataSetName()
     GetlmFitMethod()
     GetLowessType()
     GetNEWxlim(xlim)
     GetNormexpOffsetValue(CurrentNormexpOffsetValue)
     GetNumParametersNoTargets()
     getPackageVersion(pkgName)
     GetParameterizationName()
     GetParameterNames(parameterizationTreeIndex)
     GetParametersAndOrContrasts(parameterizationTreeIndex, whatFor = "heat")
     GetPlotLabels(plottitle = "", xlabel = "", ylabel = "")
     GetPlotSize()
     GetPlotTitle(plottitle = "")
     GetPValueCutoff(p.value=0.01)
     GetReducedDuplicateSpacing(parameterizationTreeIndex)
     GetRNATypesFrom.ContrastsFromDropDowns.String(string)
     GetSlideNum()
     GetSpotTypesForLinearModel()
     GetSpotTypesIncludedNames(parameterizationTreeIndex)
     GetWithinArrayNormalizationMethod()
     GetWtAreaParams()
     HeatDiagramDialog(parameterName)
     HeatDiagramPlot()
     HowManyDups()
     HTMLplotUsingFunction(Caption = "", File = .HTML.file,
                      GraphRelativeDirectory = ".", GraphAbsoluteDirectory =
                      NULL, GraphFileName = "", GraphSaveAs = "png",
                      GraphBorder = 1, Align = "center", plotFunction =
                      NULL, Width = 600, Height = 600, PointSize = 12, BG =
                      "white", res = 72, ...)
     ImageArrayPlot()
     ImageArrayPlotDialog(slidenum)
     ImportMA()
     ImportMADialog()
     initGlobals()
     InitNewParameterization()
     limmaGUI(BigfontsForlimmaGUIpresentation=FALSE)
     limmaHelp()
     limmaUsersGuide(view = TRUE)
     lmFitMethodHelp()
     LogOddsPlot()
     MAPlot()
     MAPlotAvg()
     MBoxPlot()
     MMPlot()
     NewLimmaFile()
     NormalizeNow()
     nstrstr(haystack, needle)
     onDestroy()
     onExit()
     OpenALimmaFile(FileName)
     OpenGALandTargetsandSpotTypesfiles()
     OpenGALFile()
     OpenLimmaFile()
     OpenSpotTypesFile()
     OpenTargetsFile()
     plotMAColorCoded()
     PlotOptions()
     PrintTipGroupMAPlot()
     QQTplot()
     read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
     ReadImageProcessingFiles()
     Require(pkg)
     Resize(img, plotFunction)
     SaveAsLimmaFile()
     SaveGraphAsJpeg(initialfile, plotFunction)
     SaveGraphAsPDF(initialfile, plotFunction)
     SaveGraphAsPNG(initialfile, plotFunction)
     SaveGraphAsPostscript(initialfile, plotFunction)
     SaveLimmaFile()
     SelectPlotSymbols(SpotTypes)
     SetLayoutParameters()
     SetupPlotKeyBindings(tt, img)
     SetupPlotMenus(tt, initialfile, plotFunction, img)
     SetWD()
     showChangeLog()
     showCitations()
     showGAL()
     showTopTable(..., export = FALSE)
     SimplifyContrastsExpression(string)
     strstr(haystack, needle)
     tclArrayVar()
     TclRequire(tclPkg)
     TryReadImgProcFile(expr)
     UpdateSpotTypesStatus()
     UpDownOrBoth()
     VennDiagramPlot()
     ViewDesignOrContrastsMatrixAsPairs(DesignOrContrasts, designOrContrastsList,
                      parameterizationIndex, contrastsParameterizationIndex
                      = NULL)
     ViewDesignOrContrastsMatrixInTable(DesignOrContrasts, designOrContrastsList,
                      parameterizationIndex, contrastsParameterizationIndex
                      = NULL)
     ViewExistingContrastsParameterization()
     ViewExistingParameterization()
     ViewRNATargets()
     ViewSpotTypes()

_A_r_g_u_m_e_n_t_s:

BigfontsForlimmaGUIpresentation: If set to TRUE, larger fonts are used.
           However, some font sizes are not controlled by limmaGUI and
          so must be adjusted in the operating system, e.g. in the
          Control Panel in Windows under Display, Appearance.

     ...: 

   AFile: 

   Align: 

      BG: 

 Caption: 

     cex: 

contrastsParameterizationIndex: ViewDesignOrContrastsMatrixInTable:arg4
          ,ViewDesignOrContrastsMatrixAsPairs:arg4

Contrasts: 

CurrentNormexpOffsetValue: 

designOrContrastsList: 

DesignOrContrasts: 

  Design: 

  export: 

    expr: 

FileName: 

    File: 

GraphAbsoluteDirectory: 

GraphBorder: 

GraphFileName: 

graphFileType: 

GraphRelativeDirectory: 

GraphSaveAs: 

haystack: 

  header: 

  Height: 

     img: 

   index: 

initialfile: 

itemName: 

   list1: 

   MFile: 

  needle: 

NumContrasts: 

 p.value: 

parameterizationIndex: 

parameterizationTreeIndex: 

parameterName: 

    path: 

 pkgName: 

     pkg: 

plotFunction: 

plottitle: 

PointSize: 

   quote: 

     res: 

     sep: 

slidenum: 

spotType: 

SpotTypes: 

  string: 

  tclPkg: 

      tt: 

 verbose: 

    view: 

 whatFor: 

whichCoef: 

   Width: 

  xlabel: 

    xlim: 

  ylabel: 

     {GetPlotLabels:arg3}

_D_e_t_a_i_l_s:

     This function launches a Graphical User Interface for the limma
     package by Gordon Smyth. The GUI uses Tk widgets (via the R TclTk
     interface by Peter Dalgaard) in order to provide a simple
     interface to the limma functions for linear modelling of
     microarrays and identification of differentially expressed genes.

_A_u_t_h_o_r(_s):

     James Wettenhall

