Package limmagui. July 22, 2018
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1 Package limmagui July 22, 2018 Version Date Title GUI for limma Package With Two Color Microarrays Author James Wettenhall [aut], Gordon Smyth [aut], Keith Satterley [ctb] Maintainer Gordon Smyth Imports methods, grdevices, graphics, limma, R2HTML, tcltk, tkrplot, xtable, utils Description A Graphical User Interface for differential expression analysis of twocolor microarray data using the limma package. License GPL (>=2) URL biocviews GUI, GeneExpression, DifferentialExpression, DataImport, Bayesian, Regression, TimeCourse, Microarray, mrnamicroarray, TwoChannel, BatchEffect, MultipleComparison, Normalization, Preprocessing, QualityControl git_url git_branch RELEASE_3_7 git_last_commit 31ebf8f git_last_commit_date Date/Publication R topics documented: LGchangeLog limmagui Index 8 1
2 2 limmagui LGchangeLog LimmaGUI Change Log Description Write as text the most recent changes from the limmagui package changelog. Usage LGchangeLog(n=20) Arguments n integer, number of lines to write of changelog. Value No value is produced, but a number of lines of text are written to standard output. Author(s) Gordon Smyth limmagui Graphical User Interface for the limma microarray package Description Usage Graphical User Interface for the limma microarray package 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()
3 limmagui 3 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()
4 4 limmagui 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
5 limmagui 5 = 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 Align BG Caption Flat-file of log-intensities output by marraytools HTMLplotUsingFunction:arg8 HTMLplotUsingFunction:arg13 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 export expr FileName GetDesignOrContrasts:arg1 showtoptable:arg2 TryReadImgProcFile:arg1 A file name. File HTMLplotUsingFunction:arg2 GraphAbsoluteDirectory HTMLplotUsingFunction:arg4 GraphBorder GraphFileName HTMLplotUsingFunction:arg7 HTMLplotUsingFunction:arg5 graphfiletype GetJpegOrPngParams:arg1, GetJpegOrPngX11Params:arg1 GraphRelativeDirectory HTMLplotUsingFunction:arg3 GraphSaveAs HTMLplotUsingFunction:arg6
6 6 limmagui 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, Save- GraphAsPostscript: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, Get- DesignOrContrasts:arg4, ViewDesignOrContrastsMatrixInTable:arg3, ViewDesignOrContrastsMatrixAsPairs:arg3 parameterizationtreeindex GetParametersAndOrContrasts:arg1, ChooseContrastsParameterization:arg1, ChooseSpotType:arg1,GetCoef:arg1, GetParameterNames:arg1, GetReducedDuplicateSpacing:arg1, GetContrastsParameterizationNames:arg1, GetSpotTypesIncluded- Names: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.Strin 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
7 limmagui 7 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
8 Index Topic documentation LGchangeLog, 2 AboutLimmaGUI AboutNormalization BChelp ChooseContrastsParameterization choosedir ChooseEbayesStatistic ChooseParameterization ChoosePlotSymbolByClicking ChooseSpotType ComputeContrasts ComputeLinearModelFit CopyGraph CreateNewParameterization CreateTreeAndList DeleteContrastsParameterization deleteitemfromlist DeleteParameterization DupCorBoxPlot ebayesboxplots evalrcode ExportAvalues ExportHTMLreport ExportMvalues ExportTopTable fixseps GetBackgroundCorrectionMethod GetBetweenArrayNormalizationMethod GetCoef GetComponentsToExportInHTMLreport GetContrastsParameterizationName GetContrastsParameterizationNames GetDEcutoff GetDesignOrContrasts GetGeneLabelsOptions GetGenePixFlagWeightings GetImageAnalysisColumnHeadings GetImageProcessingFileType GetJpegOrPngParams GetJpegOrPngX11Params GetlimmaDataSetName GetlmFitMethod GetLowessType GetNEWxlim GetNormexpOffsetValue GetNumParametersNoTargets getpackageversion GetParameterizationName GetParameterNames GetParametersAndOrContrasts (limmagui), 2 GetPlotLabels GetPlotSize GetPlotTitle GetPValueCutoff GetReducedDuplicateSpacing GetRNATypesFrom.ContrastsFromDropDowns.String GetSlideNum GetSpotTypesForLinearModel GetSpotTypesIncludedNames GetWithinArrayNormalizationMethod GetWtAreaParams HeatDiagramDialog HeatDiagramPlot HowManyDups HTMLplotUsingFunction ImageArrayPlot ImageArrayPlotDialog imageplotlimmagui 8
9 INDEX 9 ImportMA ImportMADialog initglobals InitNewParameterization LGchangeLog, 2 limmagui, 2 limmaguihelp limmahelp lmfitmethodhelp LogOddsPlot MAPlot MAPlotAvg MBoxPlot MMPlot NewLimmaFile NormalizeNow nstrstr ondestroy onexit OpenALimmaFile OpenGALandTargetsandSpotTypesfiles OpenGALFile OpenLimmaFile OpenSpotTypesFile OpenTargetsFile plotmacolorcoded PlotOptions PrintTipGroupMAPlot showchangelog showcitations showgal showtoptable SimplifyContrastsExpression (limmagui), 2 strstr tclarrayvar TclRequire Try TryReadImgProcFile UpdateSpotTypesStatus UpDownOrBoth venndiagramlimmagui VennDiagramPlot ViewDesignOrContrastsMatrixAsPairs ViewDesignOrContrastsMatrixInTable ViewExistingContrastsParameterization ViewExistingParameterization ViewRNATargets ViewSpotTypes WithinBetweenOrBoth wtflags2 QQTplot read.marraytools readgallimmagui ReadImageProcessingFiles Require Resize SaveAsLimmaFile SaveGraphAsJpeg SaveGraphAsPDF SaveGraphAsPNG SaveGraphAsPostscript SaveLimmaFile SelectPlotSymbols SetLayoutParameters SetupPlotKeyBindings SetupPlotMenus SetWD
Package affylmgui. July 21, 2018
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Type Package Package geecc December 7, 2018 Title Gene Set Enrichment Analysis Extended to Contingency Cubes Version 1.16.0 Date 2016-09-19 Author Markus Boenn Maintainer Markus Boenn
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Type Package Package Rbowtie2 January 21, 2019 Title An R Wrapper for Bowtie2 and AdapterRemoval Version 1.4.0 Date 2017-08-18 Author, Wei Zhang Maintainer This package provides an
Package pmg. R topics documented: March 9, Version Title Poor Man s GUI. Author John Verzani with contributions by Yvonnick Noel
Package pmg March 9, 2010 Version 0.9-42 Title Poor Man s GUI Author John Verzani with contributions by Yvonnick Noel Maintainer John Verzani Depends lattice, MASS, proto, foreign,
Package WriteXLS. March 14, 2013
Package WriteXLS March 14, 2013 Version 2.3.1 Date 2013-03-14 Title Cross-platform Perl based R function to create Excel 2003 (XLS) files Description Cross-platform Perl based R function to create Excel
Package stattarget. December 23, 2018
Type Package Title Statistical Analysis of Molecular Profiles Version 1.12.0 Author Hemi Luan Maintainer Hemi Luan Depends R (>= 3.3.0) Package stattarget December 23, 2018 Imports
Package Linnorm. October 12, 2016
Type Package Package Linnorm October 12, 2016 Title Linear model and normality based transformation method (Linnorm) Version 1.0.6 Date 2016-08-27 Author Shun Hang Yip , Panwen Wang ,
Package ERSSA. November 4, 2018
Type Package Title Empirical RNA-seq Sample Size Analysis Version 1.0.0 Date 2018-10-09 Author Zixuan Shao [aut, cre] Package ERSSA November 4, 2018 Maintainer Zixuan Shao The
Package HTMLUtils. R topics documented: February 19, Type Package
Type Package Package HTMLUtils February 19, 2015 Title Facilitates Automated HTML Report Creation Version 0.1.7 Date 2015-01-17 Depends R2HTML Suggests Author ``Markus Loecher, Berlin School of Economics
Package MEAL. August 16, 2018
Title Perform methylation analysis Version 1.11.6 Package MEAL August 16, 2018 Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several
Package barcoder. October 26, 2018
Package barcoder October 26, 2018 Title Labelling, Tracking, and Collecting Data from Biological Samples Version 0.1.0 Maintainer Robert Colautti Tools to generate unique identifiers
Package Glimma. June 29, 2018
Type Package Title Interactive HTML graphics Version 1.8.2 Date 2016-12-21 Package Glimma June 29, 2018 This package generates interactive visualisations for analysis of RNA-sequencing data using output
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Type Package Title Seamless 'D3Plus' Integration Version 0.1.0 Author Mauricio Vargas [aut,cre], Joshua Kunst [aut], Dave Landry [ctb], Datawheel [cph] Package d3plus September 25, 2017 Maintainer Mauricio
Package DMRcate. May 1, 2018
Package DMRcate May 1, 2018 Title Methylation array and sequencing spatial analysis methods Version 1.16.0 Date 2017-07-02 Author Tim Peters Maintainer Tim Peters De novo identification
Package brainr. R topics documented: October 12, Type Package
Type Package Package brainr October 12, 2017 Title Helper Functions to 'misc3d' and 'rgl' Packages for Brain Imaging Version 1.5.1 Date 2017-10-10 Maintainer John Muschelli This
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Package shinyhelper June 21, 2018 Type Package Title Easily Add Markdown Help Files to 'shiny' App Elements Version 0.3.0 BugReports https://github.com/cwthom/shinyhelper/issues Creates a lightweight way
Package cgh. R topics documented: February 19, 2015
Package cgh February 19, 2015 Version 1.0-7.1 Date 2009-11-20 Title Microarray CGH analysis using the Smith-Waterman algorithm Author Tom Price Maintainer Tom Price