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limma (version 3.28.6)

limmaGUI: Graphical User Interface for the limma microarray package

Description

Graphical User Interface for the limma microarray package

Usage

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()
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()

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.
...
HTMLplotUsingFunction:arg15, showTopTable:arg1
AFile
Flat-file of log-intensities output by marrayTools
Align
HTMLplotUsingFunction:arg8
BG
HTMLplotUsingFunction:arg13
Caption
HTMLplotUsingFunction:arg1
cex
ChoosePlotSymbolByClicking:arg2
contrastsParameterizationIndex
ViewDesignOrContrastsMatrixInTable:arg4, ViewDesignOrContrastsMatrixAsPairs:arg4
Contrasts
GetDesignOrContrasts:arg2
CurrentNormexpOffsetValue
GetNormexpOffsetValue:arg1
designOrContrastsList
ViewDesignOrContrastsMatrixInTable:arg2, ViewDesignOrContrastsMatrixAsPairs:arg2
DesignOrContrasts
ViewDesignOrContrastsMatrixInTable:arg1, ViewDesignOrContrastsMatrixAsPairs:arg1
Design
GetDesignOrContrasts:arg1
export
showTopTable:arg2
expr
TryReadImgProcFile:arg1
FileName
A file name.
File
HTMLplotUsingFunction:arg2
GraphAbsoluteDirectory
HTMLplotUsingFunction:arg4
GraphBorder
HTMLplotUsingFunction:arg7
GraphFileName
HTMLplotUsingFunction:arg5
graphFileType
GetJpegOrPngParams:arg1, GetJpegOrPngX11Params:arg1
GraphRelativeDirectory
HTMLplotUsingFunction:arg3
GraphSaveAs
HTMLplotUsingFunction:arg6
haystack
nstrstr:arg1, strstr:arg1
header
See help for read.table
Height
HTMLplotUsingFunction:arg11
img
SetupPlotMenus:arg1, Resize:arg1, CopyGraph:arg1, SetupPlotKeyBindings:arg2
index
deleteItemFromList:arg1
initialfile
SaveGraphAsJpeg:arg1, SaveGraphAsPDF:arg1, SaveGraphAsPNG:arg1, SaveGraphAsPostscript:arg1, SetupPlotMenus:arg2
itemName
deleteItemFromList:arg1
list1
deleteItemFromList:arg1
MFile
Flat-file of log-ratios output by marrayTools
needle
nstrstr:arg2, strstr:arg2
NumContrasts
GetDesignOrContrasts:arg3
p.value
A p-value cutoff.
parameterizationIndex
GetDesignOrContrasts:arg4, GetComponentsToExportInHTMLreport:arg1, GetDesignOrContrasts:arg4, ViewDesignOrContrastsMatrixInTable:arg3, ViewDesignOrContrastsMatrixAsPairs:arg3
parameterizationTreeIndex
GetParametersAndOrContrasts:arg1, ChooseContrastsParameterization:arg1, ChooseSpotType:arg1,GetCoef:arg1, GetParameterNames:arg1, GetReducedDuplicateSpacing:arg1, GetContrastsParameterizationNames:arg1, GetSpotTypesIncludedNames:arg1
parameterName
HeatDiagramDialog:arg1
path
Path to the directory containing the MFile and AFile
pkgName
getPackageVersion:arg1
pkg
Require:arg1
plotFunction
SetupPlotMenus:arg1, HTMLplotUsingFunction:arg9, Resize:arg1, SaveGraphAsJpeg:arg2, SaveGraphAsPDF:arg2, SaveGraphAsPNG:arg2, SaveGraphAsPostscript:arg2
plottitle
GetPlotLabels:arg1,GetPlotTitle:arg1
PointSize
HTMLplotUsingFunction:arg12
quote
See help for read.table
res
HTMLplotUsingFunction:arg14
sep
Column separator. ("\t" for tab-delimited text)
slidenum
ImageArrayPlotDialog:arg1
spotType
ChoosePlotSymbolByClicking:arg1
SpotTypes
SelectPlotSymbols:arg1
string
fixSeps:arg1,SimplifyContrastsExpression:arg1, GetRNATypesFrom.ContrastsFromDropDowns.String:arg1
tclPkg
TclRequire:arg1
tt
SetupPlotKeyBindings:arg1, SetupPlotMenus:arg1
verbose
Optional diagnostic messages
whatFor
GetParametersAndOrContrasts:arg2
whichCoef
GetCoef:arg2
Width
HTMLplotUsingFunction:arg10
xlabel
GetPlotLabels:arg2
xlim
GetNEWxlim:arg1
ylabel
GetPlotLabels:arg3

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.