R语言 limmaGUI包 limmaGUI()函数中文帮助文档(中英文对照)

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limmaGUI(limmaGUI)
limmaGUI()所属R语言包：limmaGUI

                                        Graphical User Interface for the limma microarray package
                                         为limma芯片封装的图形用户界面

                                         译者：生物统计家园网 机器人LoveR

描述----------Description----------

Graphical User Interface for the limma microarray package
为limma芯片封装的图形用户界面


用法----------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()
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()



参数----------Arguments----------

参数：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.
如果设置为TRUE，使用较大的字体。然而，某些字体大小不由limmaGUI控制，所以必须调整操作系统中，例如：在Windows控制面板下显示，外观。


参数：...
HTMLplotUsingFunction:arg15, showTopTable:arg1
HTMLplotUsingFunction：arg15，showTopTable的：ARG1


参数：AFile
Flat-file of log-intensities output by marrayTools
平面文件log的输出强度由marrayTools


参数：Align
HTMLplotUsingFunction:arg8
HTMLplotUsingFunction：arg8


参数：BG
HTMLplotUsingFunction:arg13
HTMLplotUsingFunction：arg13


参数：Caption
HTMLplotUsingFunction:arg1
HTMLplotUsingFunction：ARG1


参数：cex
ChoosePlotSymbolByClicking:arg2
ChoosePlotSymbolByClicking：ARG2


参数：contrastsParameterizationIndex
ViewDesignOrContrastsMatrixInTable:arg4,  ViewDesignOrContrastsMatrixAsPairs:arg4
ViewDesignOrContrastsMatrixInTable：arg4，ViewDesignOrContrastsMatrixAsPairs：arg4


参数：Contrasts
GetDesignOrContrasts:arg2
GetDesignOrContrasts：ARG2


参数：CurrentNormexpOffsetValue
GetNormexpOffsetValue:arg1
GetNormexpOffsetValue：ARG1


参数：designOrContrastsList
ViewDesignOrContrastsMatrixInTable:arg2, ViewDesignOrContrastsMatrixAsPairs:arg2
ViewDesignOrContrastsMatrixInTable：ARG2，ViewDesignOrContrastsMatrixAsPairs：ARG2


参数：DesignOrContrasts
ViewDesignOrContrastsMatrixInTable:arg1, ViewDesignOrContrastsMatrixAsPairs:arg1
ViewDesignOrContrastsMatrixInTable：ARG1，ViewDesignOrContrastsMatrixAsPairs：ARG1


参数：Design
GetDesignOrContrasts:arg1
GetDesignOrContrasts：ARG1


参数：export
showTopTable:arg2
showTopTable：ARG2


参数：expr
TryReadImgProcFile:arg1
TryReadImgProcFile：ARG1


参数：FileName
A file name.
一个文件名。


参数：File
HTMLplotUsingFunction:arg2
HTMLplotUsingFunction：ARG2


参数：GraphAbsoluteDirectory
HTMLplotUsingFunction:arg4
HTMLplotUsingFunction：arg4


参数：GraphBorder
HTMLplotUsingFunction:arg7
HTMLplotUsingFunction：arg7


参数：GraphFileName
HTMLplotUsingFunction:arg5
HTMLplotUsingFunction：arg5


参数：graphFileType
GetJpegOrPngParams:arg1, GetJpegOrPngX11Params:arg1
GetJpegOrPngParams：ARG1，GetJpegOrPngX11Params：ARG1


参数：GraphRelativeDirectory
HTMLplotUsingFunction:arg3
HTMLplotUsingFunction：arg3


参数：GraphSaveAs
HTMLplotUsingFunction:arg6
HTMLplotUsingFunction：arg6


参数：haystack
nstrstr:arg1, strstr:arg1
nstrstr：ARG1，strstr：ARG1


参数：header
See help for read.table
看到帮助的read.table


参数：Height
HTMLplotUsingFunction:arg11
HTMLplotUsingFunction：arg11


参数：img
SetupPlotMenus:arg1, Resize:arg1, CopyGraph:arg1, SetupPlotKeyBindings:arg2
SetupPlotMenus：ARG1，调整大小：ARG1，CopyGraph：ARG1，SetupPlotKeyBindings：ARG2


参数：index
deleteItemFromList:arg1
deleteItemFromList：ARG1


参数：initialfile
SaveGraphAsJpeg:arg1, SaveGraphAsPDF:arg1, SaveGraphAsPNG:arg1, SaveGraphAsPostscript:arg1, SetupPlotMenus:arg2
SaveGraphAsJpeg：ARG1，SaveGraphAsPDF：ARG1，SaveGraphAsPNG：ARG1，SaveGraphAsPostscript：ARG1，SetupPlotMenus：ARG2


参数：itemName
deleteItemFromList:arg1
deleteItemFromList：ARG1


参数：list1
deleteItemFromList:arg1
deleteItemFromList：ARG1


参数：MFile
Flat-file of log-ratios output by marrayTools
平面文件log的输出比例由marrayTools


参数：needle
nstrstr:arg2, strstr:arg2
nstrstr：ARG2，strstr：ARG2


参数：NumContrasts
GetDesignOrContrasts:arg3
GetDesignOrContrasts：arg3


参数：p.value
A p-value cutoff.
p值截止。


参数：parameterizationIndex
GetDesignOrContrasts:arg4, GetComponentsToExportInHTMLreport:arg1,  GetDesignOrContrasts:arg4, ViewDesignOrContrastsMatrixInTable:arg3, ViewDesignOrContrastsMatrixAsPairs:arg3
GetDesignOrContrasts：arg4，GetComponentsToExportInHTMLreport：ARG1，GetDesignOrContrasts：arg4，ViewDesignOrContrastsMatrixInTable：arg3，ViewDesignOrContrastsMatrixAsPairs：arg3


参数：parameterizationTreeIndex
GetParametersAndOrContrasts:arg1, ChooseContrastsParameterization:arg1, ChooseSpotType:arg1,GetCoef:arg1, GetParameterNames:arg1, GetReducedDuplicateSpacing:arg1, GetContrastsParameterizationNames:arg1, GetSpotTypesIncludedNames:arg1
GetParametersAndOrContrasts：ARG1，ChooseContrastsParameterization：ARG1，ChooseSpotType：ARG1，GetCoef：ARG1，GetParameterNames：ARG1，GetReducedDuplicateSpacing：ARG1，GetContrastsParameterizationNames：ARG1，GetSpotTypesIncludedNames：ARG1


参数：parameterName
HeatDiagramDialog:arg1
HeatDiagramDialog：ARG1


参数：path
Path to the directory containing the MFile and AFile
路径的目录包含MFile和AFile


参数：pkgName
getPackageVersion:arg1
getPackageVersion：ARG1


参数：pkg
Require:arg1
要求：ARG1


参数：plotFunction
SetupPlotMenus:arg1, HTMLplotUsingFunction:arg9, Resize:arg1, SaveGraphAsJpeg:arg2, SaveGraphAsPDF:arg2, SaveGraphAsPNG:arg2, SaveGraphAsPostscript:arg2
SetupPlotMenus：ARG1，HTMLplotUsingFunction：arg9，调整大小：ARG1，SaveGraphAsJpeg：ARG2，SaveGraphAsPDF：ARG2，SaveGraphAsPNG：ARG2，SaveGraphAsPostscript：ARG2


参数：plottitle
GetPlotLabels:arg1,GetPlotTitle:arg1
GetPlotLabels：ARG1，GetPlotTitle的：ARG1


参数：PointSize
HTMLplotUsingFunction:arg12
HTMLplotUsingFunction：arg12


参数：quote
See help for read.table
看到帮助的read.table


参数：res
HTMLplotUsingFunction:arg14
HTMLplotUsingFunction：arg14


参数：sep
Column separator. ("\t" for tab-delimited text)
列分隔。 （“\ t”的制表符分隔的文本）


参数：slidenum
ImageArrayPlotDialog:arg1
ImageArrayPlotDialog：ARG1


参数：spotType
ChoosePlotSymbolByClicking:arg1
ChoosePlotSymbolByClicking：ARG1


参数：SpotTypes
SelectPlotSymbols:arg1
SelectPlotSymbols：ARG1


参数：string
fixSeps:arg1,SimplifyContrastsExpression:arg1, GetRNATypesFrom.ContrastsFromDropDowns.String:arg1
fixSeps：ARG1，SimplifyContrastsExpression：ARG1，GetRNATypesFrom.ContrastsFromDropDowns.String：ARG1


参数：tclPkg
TclRequire:arg1
TclRequire：ARG1


参数：tt
SetupPlotKeyBindings:arg1, SetupPlotMenus:arg1
SetupPlotKeyBindings：ARG1，SetupPlotMenus：ARG1


参数：verbose
Optional diagnostic messages
可选的诊断消息


参数：view
limmaUsersGuide:arg1
limmaUsersGuide：ARG1


参数：whatFor
GetParametersAndOrContrasts:arg2
GetParametersAndOrContrasts：ARG2


参数：whichCoef
GetCoef:arg2
GetCoef：ARG2


参数：Width
HTMLplotUsingFunction:arg10
HTMLplotUsingFunction：arg10


参数：xlabel
GetPlotLabels:arg2
GetPlotLabels：ARG2


参数：xlim
GetNEWxlim:arg1
GetNEWxlim：ARG1


参数：ylabel
GetPlotLabels:arg3
GetPlotLabels：arg3


Details

详情----------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.
此功能推出一个由戈登·史密斯limma包的图形用户界面。 GUI使用Tk组件（彼得Dalgaard通过R TclTk的接口）以线性模型差异表达的基因芯片和鉴定limma功能提供了一个简单的接口。


作者（S）----------Author(s)----------


James Wettenhall

转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。


注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
注2：由于是机器人自动翻译，难免有不准确之处，使用时仔细对照中、英文内容进行反复理解，可以帮助R语言的学习。
注3：如遇到不准确之处，请在本贴的后面进行回帖，我们会逐渐进行修订。