limmaGUI {limmaGUI}R Documentation

Graphical User Interface for the limma microarray package

Description

Graphical User Interface for the limma microarray package

Usage

limmaGUI()
GetComponentsToExportInHTMLreport()
HTMLplotUsingFunction()
ExportHTMLreport()
TryReadImgProcFile()
Require()
TclRequire()
getPackageVersion()
initGlobals()
deleteItemFromList()
SetLayoutParameters()
OpenGALFile()
OpenTargetsFile()
OpenSpotTypesFile()
GetImageProcessingFileType()
ReadImageProcessingFiles()
tclArrayVar()
GetDesignOrContrasts()
SimplifyContrastsExpression()
GetRNATypesFrom.ContrastsFromDropDowns.String()
GetParameterNames()
GetReducedDuplicateSpacing()
GetContrastsParameterizationNames()
GetSpotTypesIncludedNames()
HowManyDups()
ViewDesignOrContrastsMatrixInTable()
ViewDesignOrContrastsMatrixAsPairs()
ViewExistingContrastsParameterization()
ViewExistingParameterization()
CreateNewParameterization()
ViewRNATargets()
nstrstr()
strstr()
ViewSpotTypes()
ComputeContrasts()
ComputeLinearModel()
ChooseParameterization()
GetCoef()
showTopTable()
GetSpotTypesForLinearModel()
GetSlideNum()
GetDEcutoff()
UpdateSpotTypesStatus()
ChooseEbayesStatistic()
ChooseSpotType()
GetWtAreaParams()
GetWtFlagParams()
evalRcode()
OpenGALandTargetsandSpotTypesfiles()
GetlimmaDataSetName()
GetParameterizationName()
GetContrastsParameterizationName()
ImportMA()
ImportMADialog()
NewLimmaFile()
SetWD()
onExit()
DeleteParameterization()
ChooseContrastsParameterization()
DeleteContrastsParameterization()
OpenLimmaFile()
SaveLimmaFile()
SaveAsLimmaFile()
AboutLimmaGUI()
addMenuItem()
GetMenuName()
GetNumParametersNoTargets()
AboutCustomMenu()
DeleteCustomMenuItem()
GetCustomMenuItemNum()
GetNormalizationMethod()
NormalizeNow()
AboutNormalization()
GetGeneLabelsOptions()
MAPlotAvg()
MMPlot()
GetParametersAndOrContrasts()
HeatDiagramDialog()
HeatDiagramPlot()
ImageArrayPlotDialog()
ImageArrayPlot()
LogOddsPlot()
DupCorBoxPlot()
QQTplot()
MBoxPlot()
PrintTipGroupMAPlot()
MAPlot()
ChoosePlotSymbolByClicking()
SelectPlotSymbols()
plotMAColorCoded()
GetNEWxlim()
ebayesBoxPlots()
GetPlotLabels()
GetPlotTitle()
GetPlotSize()
read.marrayTools(MFile,AFile, path, verbose, sep, quote, header, ...)
Resize()
SaveGraphAsJpeg()
SaveGraphAsPNG()
SaveGraphAsPostscript()
SaveGraphAsPDF()
showGAL()
CopyGraph()
SetupPlotKeyBindings()
SetupPlotMenus()
GetJpegOrPngParams()
GetJpegOrPngX11Params()
VennDiagramPlot()
UpDownOrBoth()
GetBackgroundCorrectionMethod()
NormalizeHelp()
BChelp()
onDestroy()
limmaGUI(BigfontsForlimmaGUIpresentation=FALSE)

Arguments

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.
MFile Flat-file of log-ratios output by marrayTools
AFile Flat-file of log-intensities output by marrayTools
path Path to the directory containing the MFile and AFile
verbose Optional diagnostic messages
sep Column separator. ("t" for tab-delimited text)
quote See help for read.table
header See help for read.table
... Any other arguments to read.marrayTools are passed to read.table

Details

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.

Author(s)

James Wettenhall


[Package Contents]