| affylmGUI {affylmGUI} | R Documentation |
Graphical User Interface for Affy analysis using the limma microarray package
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()
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. |
... |
HTMLplotUsingFunction:arg14:and:showTopTable:arg1:and:toptable2:arg9:and:vennDiagramaffylmGUI:arg6 |
Align |
HTMLplotUsingFunction:arg8 |
all |
GetSlideNum:arg1 |
BG |
HTMLplotUsingFunction:arg12 |
Caption |
HTMLplotUsingFunction:arg1 |
code |
generalPlotFunction: arg1: a code |
ContrastNames |
GetContrastNamesForHeatDiagram:arg2 |
contrastParameterizationIndex |
GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContrast:arg1:and:HTMLplotUsingFunction:arg3:and:ViewContrastsMatrixInTable:arg2 |
export |
showTopTable:arg2 |
expr |
Try:arg1:and:TryReadImgProcFile:arg1 |
File |
HTMLplotUsingFunction:arg2 |
FileName |
OpenALimmaFile:arg1 |
GraphAbsoluteDirectory |
HTMLplotUsingFunction:arg4 |
GraphBorder |
HTMLplotUsingFunction:arg7 |
GraphFileName |
HTMLplotUsingFunction:arg5 |
graphFileType |
GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1 |
GraphRelativeDirectory |
HTMLplotUsingFunction:arg3 |
GraphSaveAs |
HTMLplotUsingFunction:arg6 |
haystack |
nstrstr:arg1:and:strstr:arg1 |
Height |
HTMLplotUsingFunction:arg11 |
img |
Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2 |
includeBoth |
GetWhichProbes:arg1 |
index |
deleteItemFromList:arg3:an index |
initialfile |
SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPNG:arg1:and:SaveGraphAsPostscript:arg1 |
itemName |
deleteItemFromList:arg2:an item name |
list1 |
deleteItemFromList:arg1:a list |
needle |
nstrstr:arg2:and:strstr:arg2 |
NumContrasts |
GetContrasts:arg1 |
numContrasts |
GetContrastNamesForHeatDiagram:arg1 |
numSets |
GetSetNames:arg1 |
p.value |
GetPValueCutoff:arg1:A p-value cutoff. |
parameterName |
HeatDiagramDialog:arg1 |
pkgName |
getPackageVersion:arg1 |
pkg |
Require:arg1 |
plotFunction |
Resize:arg2:and:HTMLplotUsingFunction:arg9:and:SetupPlotMenus:arg3:and:SaveGraphAsJpeg:arg2:and:SaveGraphAsPDF:arg2:and:SaveGraphAsPNG:arg2:and:SaveGraphAsPostscript:arg2 |
plottitle |
GetPlotLabels:arg1:and:GetPlotTitle:arg1 |
res |
HTMLplotUsingFunction:arg13 |
set1 |
GetSetNames:arg2 |
set2 |
GetSetNames:arg3 |
set3 |
GetSetNames:arg4 |
string |
fixSeps:arg1:A character string:and:GetRNATypesFrom.ContrastsFromDropDowns.String:arg1:and:SimplifyContrastsExpression:arg1 |
tclPkg |
TclRequire:arg1 |
tt |
SetupPlotMenus:arg1:and:SetupPlotKeyBindings:arg1 |
view |
ALGlimmaUsersGuide:arg1:A boolean determinig if the users'd guide will be viewed |
Width |
HTMLplotUsingFunction:arg10 |
WindowTitle |
generalPlotFunction: arg2: a title |
xlabel |
GetPlotLabels:arg2 |
ylabel |
GetPlotLabels:arg3 |
fit |
topTable2:arg1:and:toptable2:arg1 |
coef |
topTable2:arg2:and:toptable2:arg2 |
number |
topTable2:arg3:and:toptable2:arg3 |
genelist |
topTable2:arg4:and:toptable2:arg4 |
A |
toptable2:arg5 |
eb |
toptable2:arg6 |
adjust.method |
topTable2:arg5:and:toptable2:arg7 |
sort.by |
topTable2:arg6:and:toptable2:arg8 |
object |
vennDiagramaffylmGUI:arg1 |
include |
vennDiagramaffylmGUI:arg2 |
names |
vennDiagramaffylmGUI:arg3 |
cex |
vennDiagramaffylmGUI:arg4 |
mar |
vennDiagramaffylmGUI:arg5 |
contrastsMatrix |
ViewContrastsMatrixAsPairs:arg1 |
contrastsMatrixList |
ViewContrastsMatrixAsPairs:arg2:and:ViewContrastsMatrixInTable:arg1 |
n |
showChangeLog:arg1 |
PointSize |
HTMLplotUsingFunction:arg12 |
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.
James Wettenhall