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

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affylmGUI(affylmGUI)
affylmGUI()所属R语言包：affylmGUI

                                        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 Affy analysis using the limma microarray package
Affy分析的图形用户界面使用limma芯片封装


用法----------Usage----------


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()
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()



参数----------Arguments----------

参数：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.
affylmGUI：ARG1：如果设置为TRUE，使用较大的字体。然而，某些字体大小不由affylmGUI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:arg14:and:showTopTable:arg1:and:toptable2:arg9:and:vennDiagramaffylmGUI:arg6
HTMLplotUsingFunction：arg14：和：showTopTable：ARG1：和：toptable2：arg9：：vennDiagramaffylmGUI：arg6


参数：Align
HTMLplotUsingFunction:arg8
HTMLplotUsingFunction：arg8


参数：all
GetSlideNum:arg1
GetSlideNum：ARG1


参数：BG
HTMLplotUsingFunction:arg12
HTMLplotUsingFunction：arg12


参数：Caption
HTMLplotUsingFunction:arg1
HTMLplotUsingFunction：ARG1


参数：code
generalPlotFunction: arg1: a code
generalPlotFunction：ARG1：代码


参数：ContrastNames
GetContrastNamesForHeatDiagram:arg2
GetContrastNamesForHeatDiagram：ARG2


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



参数：export
showTopTable:arg2
showTopTable：ARG2


参数：expr
Try:arg1:and:TryReadImgProcFile:arg1
尝试：ARG1：TryReadImgProcFile：ARG1


参数：File
HTMLplotUsingFunction:arg2
HTMLplotUsingFunction：ARG2


参数：FileName
OpenALimmaFile:arg1
OpenALimmaFile：ARG1


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:and:GetJpegOrPngX11Params:arg1
GetJpegOrPngParams：ARG1：和：GetJpegOrPngX11Params的：ARG1


参数：GraphRelativeDirectory
HTMLplotUsingFunction:arg3
HTMLplotUsingFunction：arg3


参数：GraphSaveAs
HTMLplotUsingFunction:arg6
HTMLplotUsingFunction：arg6


参数：haystack
nstrstr:arg1:and:strstr:arg1
nstrstr：ARG1：strstr：ARG1


参数：Height
HTMLplotUsingFunction:arg11
HTMLplotUsingFunction：arg11


参数：img
Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2
调整大小：ARG1：和：SetupPlotMenus：arg4：：CopyGraph：ARG1：和：SetupPlotKeyBindings：ARG2


参数：includeBoth
GetWhichProbes:arg1
GetWhichProbes：ARG1


参数：index
deleteItemFromList:arg3:an index
deleteItemFromList：arg3：索引


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



参数：itemName
deleteItemFromList:arg2:an item name
deleteItemFromList：ARG2：项目名称


参数：list1
deleteItemFromList:arg1:a list
deleteItemFromList：ARG1：列表


参数：needle
nstrstr:arg2:and:strstr:arg2
nstrstr：的ARG2：和：strstr：ARG2


参数：NumContrasts
GetContrasts:arg1
GetContrasts：ARG1


参数：numContrasts
GetContrastNamesForHeatDiagram:arg1
GetContrastNamesForHeatDiagram：ARG1


参数：numSets
GetSetNames:arg1
GetSetNames：ARG1


参数：p.value
GetPValueCutoff:arg1:A p-value cutoff.
GetPValueCutoff：ARG1：p值截止。


参数：parameterName
HeatDiagramDialog:arg1
HeatDiagramDialog：ARG1


参数：pkgName
getPackageVersion:arg1
getPackageVersion：ARG1


参数：pkg
Require:arg1
要求：ARG1


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



参数：plottitle
GetPlotLabels:arg1:and:GetPlotTitle:arg1
GetPlotLabels：ARG1：GetPlotTitle：ARG1


参数：res
HTMLplotUsingFunction:arg13
HTMLplotUsingFunction：arg13


参数：set1
GetSetNames:arg2
GetSetNames：ARG2


参数：set2
GetSetNames:arg3
GetSetNames：arg3


参数：set3
GetSetNames:arg4
GetSetNames：arg4


参数：string
fixSeps:arg1:A character string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1
：ARG1：fixSeps字符串：GetRNATypesFrom.ContrastsFromDropDowns.String：ARG1：SimplifyContrastsExpression：ARG1


参数：tclPkg
TclRequire:arg1
TclRequire：ARG1


参数：tt
SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1
SetupPlotMenus：ARG1：和：SetupPlotKeyBindings的：ARG1


参数：view
ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd guide will be viewed
ALGlimmaUsersGuide：ARG1：一个布尔值，同时测定，如果usersd指南将被视为


参数：Width
HTMLplotUsingFunction:arg10
HTMLplotUsingFunction：arg10


参数：WindowTitle
generalPlotFunction: arg2: a title
generalPlotFunction：ARG2：标题


参数：xlabel
GetPlotLabels:arg2
GetPlotLabels：ARG2


参数：ylabel
GetPlotLabels:arg3
GetPlotLabels：arg3


参数：fit
topTable2:arg1:and:toptable2:arg1
topTable2：ARG1：和：toptable2：ARG1


参数：coef
topTable2:arg2:and:toptable2:arg2
topTable2：ARG2：toptable2：ARG2


参数：number
topTable2:arg3:and:toptable2:arg3
topTable2：arg3：和：toptable2：arg3


参数：genelist
topTable2:arg4:and:toptable2:arg4
topTable2：arg4：和：toptable2：arg4


参数：A
toptable2:arg5
toptable2：arg5


参数：eb
toptable2:arg6
toptable2：arg6


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


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


参数：object
vennDiagramaffylmGUI:arg1
vennDiagramaffylmGUI：ARG1


参数：include
vennDiagramaffylmGUI:arg2
vennDiagramaffylmGUI：ARG2


参数：names
vennDiagramaffylmGUI:arg3
vennDiagramaffylmGUI：arg3


参数：cex
vennDiagramaffylmGUI:arg4
vennDiagramaffylmGUI：arg4


参数：mar
vennDiagramaffylmGUI:arg5
vennDiagramaffylmGUI：arg5


参数：contrastsMatrix
ViewContrastsMatrixAsPairs:arg1
ViewContrastsMatrixAsPairs：ARG1


参数：contrastsMatrixList
ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1
ViewContrastsMatrixAsPairs：ARG2：ViewContrastsMatrixInTable：ARG1


参数：n
showChangeLog:arg1
showChangeLog：ARG1


参数：PointSize
HTMLplotUsingFunction:arg12
HTMLplotUsingFunction：arg12


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。
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