Graphical User Interface for the limma microarray package

Description

Graphical User Interface for the limma microarray package

Usage

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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.

Author(s)

James Wettenhall

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