Package affylmgui. July 21, 2018
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1 Version Date Package affylmgui July 21, 2018 Title GUI for limma Package with Affymetrix Microarrays Author James Wettenhall [cre,aut], Ken Simpson [aut], Gordon Smyth [aut], Keith Satterley [ctb] Maintainer Gordon Smyth Imports grdevices, graphics, stats, utils, tcltk, tkrplot, limma, affy, affyio, affyplm, gcrma, BiocGenerics, BiocInstaller, R2HTML, xtable Description A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages. License GPL (>=2) URL biocviews GUI, GeneExpression, Transcription, DifferentialExpression, DataImport, Bayesian, Regression, TimeCourse, Microarray, mrnamicroarray, OneChannel, ProprietaryPlatforms, BatchEffect, MultipleComparison, Normalization, Preprocessing, QualityControl git_url git_branch RELEASE_3_7 git_last_commit 27ace1f git_last_commit_date Date/Publication R topics documented: affylmgui ALGchangeLog Index 7 1
2 2 affylmgui affylmgui Graphical User Interface for the limma microarray package Description Usage 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="")
3 affylmgui 3 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 = ".", GraphAbsolute 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)
4 4 affylmgui 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", s Try(expr) TryReadImgProcFile(expr) UpDownOrBoth() venndiagramaffylmgui(object, include = "both", names, cex = 1.5, mar = rep(1, 4),...) VennDiagramPlot() ViewContrastsMatrixAsPairs(contrastsMatrix, contrastsmatrixlist,contrastparameterizationindex = N ViewContrastsMatrixInTable(contrastsMatrixList, contrastparameterizationindex = NULL) ViewExistingContrastParameterization() ViewRNATargets() Arguments 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:vennDiagramaffylm Align all BG Caption code HTMLplotUsingFunction:arg8 GetSlideNum:arg1 HTMLplotUsingFunction:arg12 HTMLplotUsingFunction:arg1 generalplotfunction: arg1: a code ContrastNames GetContrastNamesForHeatDiagram:arg2 contrastparameterizationindex GetComponentsToExportInHTMLreport:arg1:and:contrastParameterizationIndex:arg1:and:GetContr export expr File showtoptable:arg2 Try:arg1:and:TryReadImgProcFile:arg1 HTMLplotUsingFunction:arg2 FileName OpenALimmaFile:arg1 GraphAbsoluteDirectory HTMLplotUsingFunction:arg4 GraphBorder GraphFileName HTMLplotUsingFunction:arg7 HTMLplotUsingFunction:arg5 graphfiletype GetJpegOrPngParams:arg1:and:GetJpegOrPngX11Params:arg1 GraphRelativeDirectory HTMLplotUsingFunction:arg3 GraphSaveAs haystack Height img includeboth HTMLplotUsingFunction:arg6 nstrstr:arg1:and:strstr:arg1 HTMLplotUsingFunction:arg11 Resize:arg1:and:SetupPlotMenus:arg4:and:CopyGraph:arg1:and:SetupPlotKeyBindings:arg2 GetWhichProbes:arg1
5 affylmgui 5 index deleteitemfromlist:arg3:an index initialfile SetupPlotMenus:arg2:and:SaveGraphAsJpeg:arg1:and:SaveGraphAsPDF:arg1:and:SaveGraphAsPN 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:arg 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:s 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
6 6 ALGchangeLog 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 ALGchangeLog affylmgui Change Log Description Write as text the most recent changes from the affylmgui package changelog. Usage ALGchangeLog(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
7 Index Topic IO affylmgui, 2 Topic documentation ALGchangeLog, 6 AboutaffylmGUI affyhelp affylmgui, 2 affylmguihelp affyplotma affyplotmacontrast ALGchangeLog, 6 ALGlimmaUsersGuide ChooseCDF ChooseContrastParameterization choosedir ChooseEbayesStatistic ComputeContrasts ComputeLinearModelFit CopyGraph DeleteContrastParameterization deleteitemfromlist DensityPlot DensityPlotAll evalrcode ExportHTMLreport ExportNormalizedExpressionValues ExportTopTable fixseps generalplotfunction GetComponentsToExportInHTMLreport GetContrast GetContrastNamesForHeatDiagram GetContrastParameterizationName GetContrasts GetDEcutoff GetGeneLabelsOptions GetJpegOrPngParams GetJpegOrPngX11Params GetlimmaDataSetName GetLogPLMDataChoice GetMultipleContrasts GetNormalizationMethod getpackageversion GetParameterizationName GetPlotLabels GetPlotSize GetPlotTitle GetPValueCutoff GetResidualTypeChoice GetRNATypesFrom.ContrastsFromDropDowns.String GetSetNames GetSlideNum GetSlideNums GetWhichProbes GetWtAreaParams GetWtFlagParams HeatDiagramDialog HeatDiagramPlot HTMLplotUsingFunction ImageArrayPlot ImageQualityResidualPlot ImageQualityWeightPlot initglobals IntensityHistogram IntensityHistogramAll limmahelp LogOddsPlot NewLimmaFile NormalizedIntensityBoxPlot (affylmgui), 2 NormalizeNow nstrstr 7
8 8 INDEX NUSEPlotAll ondestroy onexit OpenALimmaFile OpenCDFandTargetsfiles OpenCDFFile OpenLimmaFile OpenTargetsFile PlotOptions QQTplot RawIntensityBoxPlot Require Resize RLEPlotAll RNADegradationPlotAll SaveAsLimmaFile SaveGraphAsJpeg SaveGraphAsPDF SaveGraphAsPNG SaveGraphAsPostscript SaveLimmaFile SetupPlotKeyBindings SetupPlotMenus SetWD showchangelog showcitations showtoptable SimplifyContrastsExpression strstr tclarrayvar TclRequire toptable2 toptable2 Try TryReadImgProcFile UpDownOrBoth venndiagramaffylmgui VennDiagramPlot ViewContrastsMatrixAsPairs (affylmgui), 2 ViewContrastsMatrixInTable (affylmgui), 2 ViewExistingContrastParameterization ViewRNATargets
Package limmagui. July 22, 2018
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Version 1.5.0 Date 2018-10-26 Package SingleCellExperiment Title S4 Classes for Single Cell Data Depends R (>= 3.5), SummarizedExperiment December 13, 2018 Imports S4Vectors, methods, BiocGenerics, utils,
Package ConsensusClusterPlus
Type Package Package ConsensusClusterPlus October 1, 2018 Imports Biobase, ALL, graphics, stats, utils, cluster Title ConsensusClusterPlus Version 1.44.0 Date 2015-12-29 Author Matt Wilkerson ,
Package bumphunter. September 22, 2018
Package bumphunter September 22, 2018 Version 1.22.0 Title Bump Hunter Tools for finding bumps in genomic data Depends R (>= 3.4), S4Vectors (>= 0.9.25), IRanges (>= 2.3.23), GenomeInfoDb, GenomicRanges,
Package roar. August 31, 2018
Type Package Package roar August 31, 2018 Title Identify differential APA usage from RNA-seq alignments Version 1.16.0 Date 2016-03-21 Author Elena Grassi Maintainer Elena Grassi Identify
Package methylgsa. March 7, 2019
Package methylgsa March 7, 2019 Type Package Title Gene Set Analysis Using the Outcome of Differential Methylation Version 1.1.3 The main functions for methylgsa are methylglm and methylrra. methylgsa
Package ENmix. September 17, 2015
Version 1.0.0 Date 2015-04-15 Package ENmix September 17, 2015 Title Data preprocessing and quality control for Illumina HumanMethylation450 BeadChip Type Package Illumina HumanMethylation450 BeadChip
Package GSVA. R topics documented: January 22, Version
Version 1.26.0 Package GSVA January 22, 2018 Title Gene Set Variation Analysis for microarray and RNA-seq data Depends R (>= 3.0.0) Imports methods, BiocGenerics, Biobase, GSEABase (>= 1.17.4), geneplotter,
Package INCATome. October 5, 2017
Type Package Package INCATome October 5, 2017 Title Internal Control Analysis of Translatome Studies by Microarrays Version 1.0 Date 2017-10-03 Author Sbarrato T. [cre,aut], Spriggs R.V. [cre,aut], Wilson
Package slickr. March 6, 2018
Version 0.2.4 Date 2018-01-17 Package slickr March 6, 2018 Title Create Interactive Carousels with the JavaScript 'Slick' Library Create and customize interactive carousels using the 'Slick' JavaScript
Introduction: microarray quality assessment with arrayqualitymetrics
: microarray quality assessment with arrayqualitymetrics Audrey Kauffmann, Wolfgang Huber October 30, 2017 Contents 1 Basic use............................... 3 1.1 Affymetrix data - before preprocessing.............
Package SC3. September 29, 2018
Type Package Title Single-Cell Consensus Clustering Version 1.8.0 Author Vladimir Kiselev Package SC3 September 29, 2018 Maintainer Vladimir Kiselev A tool for unsupervised
Package enrichplot. September 29, 2018
Package enrichplot September 29, 2018 Title Visualization of Functional Enrichment Result Version 1.1.7 The 'enrichplot' package implements several visualization methods for interpreting functional enrichment
Package comphclust. February 15, 2013
Package comphclust February 15, 2013 Version 1.0-1 Date 2010-02-27 Title Complementary Hierarchical Clustering Author Gen Nowak and Robert Tibshirani Maintainer Gen Nowak Description