affylmGUI             package:affylmGUI             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 Affy analysis using the limma
     microarray package

_U_s_a_g_e:

     AboutaffylmGUI()
     affyHelp()
     affylmGUI(BigfontsForaffylmGUIpresentation=FALSE)
     affylmGUIhelp()
     affyPlotMA()
     affyPlotMAcontrast()
     ALGlimmaUsersGuide(view=TRUE)
     ChooseCDF()
     ChooseContrastParameterization()
     chooseDir()
     ChooseEbayesStatistic()
     ComputeContrasts()
     ComputeLinearModelFit()
     CopyGraph(img)
     DeleteContrastParameterization()
     deleteItemFromList(list1,itemName=NULL,index=NULL)
     DensityPlot()
     DensityPlotAll()
     evalRcode()
     ExportHTMLreport()
     ExportNormalizedExpressionValues()
     ExportTopTable()
     fixSeps(string)
     generalPlotFunction(code="",WindowTitle="")
     GetComponentsToExportInHTMLreport(contrastParameterizationIndex=NULL)
     GetContrast(contrastParameterizationIndex)
     GetContrastNamesForHeatDiagram(numContrasts=2,ContrastNames=c("Contrast 1","Contrast 2"))
     GetContrastParameterizationName()
     GetContrasts(NumContrasts=0)
     GetDEcutoff()
     GetGeneLabelsOptions()
     GetJpegOrPngParams(graphFileType)
     GetJpegOrPngX11Params(graphFileType)
     GetlimmaDataSetName()
     GetLogPLMDataChoice()
     GetMultipleContrasts(contrastParameterizationIndex)
     GetNormalizationMethod()
     getPackageVersion(pkgName)
     GetParameterizationName()
     GetPlotLabels(plottitle="",xlabel="",ylabel="")
     GetPlotSize()
     GetPlotTitle(plottitle="")
     GetPValueCutoff(p.value=0.01)
     GetResidualTypeChoice()
     GetRNATypesFrom.ContrastsFromDropDowns.String(string)
     GetSetNames(numSets=2,set1="",set2="",set3="")
     GetSlideNum(all=FALSE)
     GetSlideNums()
     GetWhichProbes(includeBoth=FALSE)
     GetWtAreaParams()
     GetWtFlagParams()
     HeatDiagramDialog(parameterName)
     HeatDiagramPlot()
     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()
     ImageQualityResidualPlot()
     ImageQualityWeightPlot()
     initGlobals()
     IntensityHistogram()
     IntensityHistogramAll()
     limmaHelp()
     LogOddsPlot()
     NewLimmaFile()
     NormalizedIntensityBoxPlot()
     NormalizeNow()
     nstrstr(haystack,needle)
     NUSEPlotAll()
     onDestroy()
     onExit()
     OpenALimmaFile(FileName)
     OpenCDFandTargetsfiles()
     OpenCDFFile()
     OpenLimmaFile(FileName)
     OpenTargetsFile()
     PlotOptions()
     QQTplot()
     RawIntensityBoxPlot()
     Require(pkg)
     Resize(img,plotFunction)
     RLEPlotAll()
     RNADegradationPlotAll()
     SaveAsLimmaFile()
     SaveGraphAsJpeg(initialfile, plotFunction)
     SaveGraphAsPDF(initialfile, plotFunction)
     SaveGraphAsPNG(initialfile, plotFunction)
     SaveGraphAsPostscript(initialfile, plotFunction)
     SaveLimmaFile()
     SetupPlotKeyBindings(tt,img)
     SetupPlotMenus(tt,initialfile,plotFunction,img)
     SetWD()
     showChangeLog(n = 20)
     showCitations()
     showTopTable(...,export=FALSE)
     SimplifyContrastsExpression(string)
     strstr(haystack, needle)
     tclArrayVar()
     TclRequire(tclPkg)
     topTable2(fit, coef = 1, number = 10, genelist = NULL,adjust.method = "holm", sort.by = "B")
     toptable2(fit, coef = 1, number = 10, genelist = NULL, A = NULL,eb = NULL, adjust.method = "holm", sort.by = "B", ...)
     Try(expr)
     TryReadImgProcFile(expr)
     UpDownOrBoth()
     vennDiagramaffylmGUI(object, include = "both", names, cex = 1.5, mar = rep(1, 4), ...)
     VennDiagramPlot()
     ViewContrastsMatrixAsPairs(contrastsMatrix, contrastsMatrixList,contrastParameterizationIndex = NULL)
     ViewContrastsMatrixInTable(contrastsMatrixList, contrastParameterizationIndex = NULL)
     ViewExistingContrastParameterization()
     ViewRNATargets()

_A_r_g_u_m_e_n_t_s:

BigfontsForaffylmGUIpresentation: affylmGUI:arg1:If set to TRUE, larger
          fonts are used.  However, some font sizes are not controlled
          by affylmGUI and so must be adjusted in the operating system,
          e.g. in the Control Panel in Windows under Display,
          Appearance.

     ...: 
          HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:toptable2:arg9:and:vennDiagramaffylmGUI:arg6

   Align: HTMLplotUsingFunction:arg8

     all: GetSlideNum:arg1

      BG: HTMLplotUsingFunction:arg12

 Caption: HTMLplotUsingFunction:arg1

    code: generalPlotFunction: arg1: a code

ContrastNames: GetContrastNamesForHeatDiagram:arg2

contrastParameterizationIndex: 
          GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContrast:arg1:and:HTMLplotUsingFunction:arg3:and:ViewContrastsMatrixInTable:arg2

  export: showTopTable:arg2

    expr: Try:arg1:and:TryReadImgProcFile:arg1

FileName: OpenALimmaFile:arg1:and:OpenLimmaFile:arg1

    File: HTMLplotUsingFunction:arg2

GraphAbsoluteDirectory: HTMLplotUsingFunction:arg4

GraphBorder: HTMLplotUsingFunction:arg7

GraphFileName: HTMLplotUsingFunction:arg5

graphFileType: GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1

GraphRelativeDirectory: HTMLplotUsingFunction:arg3

GraphSaveAs: HTMLplotUsingFunction:arg6

haystack: nstrstr:arg1:and:strstr:arg1

  Height: HTMLplotUsingFunction:arg11

     img: 
          Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2

includeBoth: GetWhichProbes:arg1

   index: deleteItemFromList:arg3:an index

initialfile: 
          SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1

itemName: deleteItemFromList:arg2:an item name

   list1: deleteItemFromList:arg1:a list

  needle: nstrstr:arg2:and:strstr:arg2

NumContrasts: GetContrasts:arg1

numContrasts: GetContrastNamesForHeatDiagram:arg1

 numSets: GetSetNames:arg1

 p.value: GetPValueCutoff:arg1:A p-value cutoff.

parameterName: HeatDiagramDialog:arg1

 pkgName: getPackageVersion:arg1

     pkg: Require:arg1

plotFunction: 
          Resize:arg2:and:HTMLplotUsingFunction:arg9:and:SetupPlotMenus:arg3:and:SaveGraphAsJpeg:arg2:and:SaveGraphAsPDF:arg2:and:SaveGraphAsPNG:arg2:and:SaveGraphAsPostscript:arg2

plottitle: GetPlotLabels:arg1:and:GetPlotTitle:arg1

     res: HTMLplotUsingFunction:arg13

    set1: GetSetNames:arg2

    set2: GetSetNames:arg3

    set3: GetSetNames:arg4

  string: fixSeps:arg1:A character
          string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1

  tclPkg: TclRequire:arg1

      tt: SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1

    view: ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd
          guide will be viewed

   Width: HTMLplotUsingFunction:arg10

WindowTitle: generalPlotFunction: arg2: a title

  xlabel: GetPlotLabels:arg2

  ylabel: GetPlotLabels:arg3

     fit: topTable2:arg1:and:toptable2:arg1

    coef: topTable2:arg2:and:toptable2:arg2

  number: topTable2:arg3:and:toptable2:arg3

genelist: topTable2:arg4:and:toptable2:arg4

       A: toptable2:arg5

      eb: toptable2:arg6

adjust.method: topTable2:arg5:and:toptable2:arg7

 sort.by: topTable2:arg6:and:toptable2:arg8

  object: vennDiagramaffylmGUI:arg1

 include: vennDiagramaffylmGUI:arg2

   names: vennDiagramaffylmGUI:arg3

     cex: vennDiagramaffylmGUI:arg4

     mar: vennDiagramaffylmGUI:arg5

contrastsMatrix: ViewContrastsMatrixAsPairs:arg1

contrastsMatrixList: 
          ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1

       n: showChangeLog:arg1

PointSize: HTMLplotUsingFunction:arg12

_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

