Package`aroma.core'January6,2016Version3.0.0DependsR(=3.1.2),R.utils - PDF document

Package`aroma.core'February4,2020Version3.2.1DependsR�(=3.2.1),R.utils�(=2.9.0),R.lesets�(=2.13.0),R.devices�(=2.16.0)DependsNoteBioC�(=3.0)Importsstats,utils,R.methodsS3�(=1.7.1),R.oo�(=1.23.0),R.cache�(=0.14.0),R.rsp�(=0.43.2),matrixStats�(=0.55.0),RColorBrewer�(=1.1-2),PSCBS�(=0.65.0),listenv,future,BiocManagerSuggestsKernSmooth,png�(=0.1-7),Cairo�(=1.5-9),EBImage�(=4.8.3),preprocessCore�(=1.28.0),aroma.light�(=2.2.1),DNAcopy�(=1.40.0),GLAD�(=2.30.0),st�(=0.1.8),expectile�(=0.2.5),HaarSeg�(=0.0.2),mpcbs�(=1.1.1)SuggestsNoteBioC�(=3.0),Recommended:aroma.light,DNAcopy,png,preprocessCore,stAdditional_repositorieshttps://r-forge.r-project.org,https://henrikbengtsson.github.io/dratTitleCoreMethodsandClassesUsedbyaroma.*PackagesPartoftheAromaFrameworkDescriptionCoremethodsandclassesusedbyhigher-levelaroma.*packagespartoftheAromaProject,e.g.aroma.affymetrixandaroma.cn.LicenseLGPL�(=2.1)URLhttps://github.com/HenrikBengtsson/aroma.core,https://www.aroma-project.org/BugReportshttps://github.com/HenrikBengtsson/aroma.core/issuesLazyLoadTRUEbiocViewsMicroarray,OneChannel,TwoChannel,MultiChannel,DataImport,DataRepresentation,GUI,Visualization,Preprocessing,QualityControl,aCGH,CopyNumberVariantsNeedsCompilationno1 2Rtopicsdocumented:AuthorHenrikBengtsson[aut,cre,cph],MarkRobinson[ctb],KenSimpson[ctb]MaintainerHenrikBengtsson&#xhenr;&#xikb@;raj;&#xu.co;&#xm000;RepositoryCRANDate/Publication2020-02-0415:20:21UTCRtopicsdocumented:aroma.core-package.....................................3AbstractCNData.......................................4AbstractPSCNData.....................................6AromaCellCpgFile.....................................7AromaCellPositionFile...................................8AromaCellTabularBinaryFile................................9AromaGenomeTextFile...................................11AromaMicroarrayDataFile.................................14AromaMicroarrayDataSet..................................15AromaMicroarrayDataSetTuple..............................17AromaMicroarrayTabularBinaryFile............................18AromaPlatform.......................................21AromaPlatformInterface..................................22AromaRepository......................................23AromaTabularBinaryFile..................................25AromaTabularBinarySet..................................27AromaTransform......................................29AromaUnitCallFile.....................................30AromaUnitCallSet.....................................32AromaUnitFracBCnBinaryFile...............................34AromaUnitFracBCnBinarySet...............................37AromaUnitGenotypeCallFile................................39AromaUnitGenotypeCallSet................................41AromaUnitPscnBinaryFile.................................43AromaUnitPscnBinarySet..................................46AromaUnitSignalBinaryFile................................48AromaUnitSignalBinarySet.................................50AromaUnitTabularBinaryFile................................52AromaUnitTotalCnBinaryFile...............................54AromaUnitTotalCnBinarySet................................57AromaUnitTypesFile....................................59BinnedScatter........................................61CbsModel..........................................63ChromosomalModel....................................65ChromosomeExplorer....................................66colBinnedSmoothing.matrix................................68colKernelSmoothing.matrix.................................71CopyNumberChromosomalModel.............................73 aroma.core-package3CopyNumberSegmentationModel.............................74doCBS............................................76Explorer...........................................77GladModel.........................................78HaarSegModel.......................................80NonPairedPSCNData....................................82PairedPSCNData......................................84ParametersInterface.....................................87RawAlleleBFractions....................................88RawCopyNumberModel..................................89RawCopyNumbers.....................................91RawGenomicSignals....................................94RawMirroredAlleleBFractions...............................97RawSequenceReads.....................................98SegmentedAlleleBFractions................................100SegmentedCopyNumbers..................................102SegmentedGenomicSignalsInterface............................105UnitAnnotationDataFile..................................106UnitNamesFile.......................................107UnitTypesFile........................................108Index110 aroma.core-packagePackagearoma.core DescriptionCoremethodsandclassesusedbyhigher-level'aroma.*'packagespartoftheAromaProject,e.g.'aroma.affymetrix'and'aroma.cn'.Thispackageisasupportpackageforaroma.affymetrix.Thispackageshouldbeconsideredtobeinanalphaorbetaphase.YoushouldexpecttheAPItobechangingovertime.Forpracticalpurposes,considerthispackageaprivatepackage.InstallationandupdatesThispackageisavailableonCRAN,i.e.toinstalldoinstall.packages("aroma.core").LicenseThereleasesofthispackageislicensedunderLGPLversion2.1ornewer.Thedevelopmentcodeofthepackagesisunderaprivatelicence(whereapplicable)andpatchessenttotheauthorfallunderthelatterlicense,butwillbe,ifincorporated,releasedunderthe"release"licenseabove.Author(s)HenrikBengtsson 4AbstractCNDataReferences[1]H.Bengtsson,TheR.oopackage-Object-OrientedProgrammingwithReferencesUsingStan-dardRCode,InKurtHornik,FriedrichLeischandAchimZeileis,editors,Proceedingsofthe3rdInternationalWorkshoponDistributedStatisticalComputing(DSC2003),March20-22,Vienna,Austria.http://www.ci.tuwien.ac.at/Conferences/DSC-2003/Proceedings/ AbstractCNDataTheAbstractCNDataclass DescriptionPackage:aroma.coreClassAbstractCNDatadata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--AbstractCNDataDirectlyknownsubclasses:AbstractPSCNData,NonPairedPSCNData,PairedPSCNDatapublicclassAbstractCNDataextendsRawGenomicSignalsAnAbstractCNDataobjectholdscopynumberdata.UsageAbstractCNData(chromosome=NULL,x=NULL,y=NULL,...,name=NULL,.virtuals=NULL)Argumentschromosome(Optional)Anintegerscalar(oravectoroflengthJ),whichcanbeusedtospecifywhichchromosomeeachlocusbelongstoincasemultiplechromosomesaresegments.Thisargumentisalsousedforannotationpurposes.xOptionalnumericvectorofJgenomiclocations.IfNULL,indexlocations1:Jareused.yOptionalnumericvectorofJgenomiclocations....Optionalnamedlocus-specicsignalvectorsoflengthJ.nameOptionalcharacterstring..virtuals(Internal)alistwithvirtualcolumnnamefunctions. AbstractCNData5FieldsandMethodsMethods:findLargeGaps-getChipType-getLocusData-getPlatform-setChipType-setPlatform-MethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,print,prompt,rbind,row.names,row.namesrow-sum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson 6AbstractPSCNData AbstractPSCNDataTheAbstractPSCNDataclass DescriptionPackage:aroma.coreClassAbstractPSCNDatadata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--AbstractCNData~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AbstractPSCNDataDirectlyknownsubclasses:NonPairedPSCNData,PairedPSCNDatapublicclassAbstractPSCNDataextendsAbstractCNDataAAbstractPSCNDataobjectholdsparent-speciccopynumberdata.UsageAbstractPSCNData(chromosome=NULL,x=NULL,isSNP=NULL,mu=NULL,...)Argumentschromosome(Optional)Anintegerscalar(oravectoroflengthJ),whichcanbeusedtospecifywhichchromosomeeachlocusbelongstoincasemultiplechromosomesaresegments.Thisargumentisalsousedforannotationpurposes.xOptionalnumericvectorofJgenomiclocations.IfNULL,indexlocations1:Jareused.isSNPAnoptionallogicalvectoroflengthJspecifyingwhethereachlocusisaSNPornot(non-polymorphicloci).muAnoptionalnumericvectorofJgenotypecallsin{0,1/2,1}forAA,AB,andBB,respectively,andNAfornon-polymorphicloci....Optionalnamedlocus-specicsignalvectorsoflengthJ. AromaCellCpgFile7FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromAbstractCNData:ndLargeGaps,getChipType,getLocusData,getPlatform,hasKnownPositions,orderAlongGenome,setChipType,setPlatformMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,print,prompt,rbind,row.names,row.namesrow-sum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson AromaCellCpgFileAbinaryleholdinglocalCpGdensityforeachcell(probe/feature) DescriptionAbinaryleholdinglocalCpGdensityforeachcell(probe/feature). 8AromaCellPositionFileUsageAromaCellCpgFile(...)Arguments...ArgumentspassedtoconstructorofAromaCellTabularBinaryFile.DetailsNotethatthisclassdoesnotassumearectangularchiplayout.Inotherwords,thereisnoconceptofmappingaspatiallocationonthearraytoacellindexandviceversa.Thereasonforthistobeabletousethisclassalsofornon-rectangularchiptypes.Author(s)MarkRobinson AromaCellPositionFileAbinaryleholdingchromosome/positionforeachcell DescriptionAbinaryleholdingchromosome/positionforeachcell.UsageAromaCellPositionFile(...)Arguments...ArgumentspassedtoconstructorofAromaCellTabularBinaryFile.DetailsNotethatthisclassdoesnotassumearectangularchiplayout.Inotherwords,thereisnoconceptofmappingaspatiallocationonthearraytoacellindexandviceversa.Thereasonforthistobeabletousethisclassalsofornon-rectangularchiptypes.Author(s)HenrikBengtsson AromaCellTabularBinaryFile9 AromaCellTabularBinaryFileTheAromaCellTabularBinaryFileclass DescriptionPackage:aroma.coreClassAromaCellTabularBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaCellTabularBinaryFileDirectlyknownsubclasses:AromaCellCpgFile,AromaCellPositionFile,AromaCellSequenceFilepublicabstractstaticclassAromaCellTabularBinaryFileextendsAromaMicroarrayTabularBinaryFileAnAromaCellTabularBinaryFileisanAromaTabularBinaryFilewiththeconstraintthattherowsmapone-to-onetothecells(features)ofamicroarray.UsageAromaCellTabularBinaryFile(...) 10AromaCellTabularBinaryFileArguments...ArgumentspassedtoAromaTabularBinaryFile.FieldsandMethodsMethods:byChipType-nbrOfCells-MethodsinheritedfromAromaMicroarrayTabularBinaryFile:allocate,as.character,byChipType,ndByChipType,getChipType,getFilenameExtension,getPlat-formMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentName AromaGenomeTextFile11MethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonSeeAlsoAromaUnitTabularBinaryFile. AromaGenomeTextFileTheAromaGenomeTextFileclass DescriptionPackage:aroma.coreClassAromaGenomeTextFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--TabularTextFile~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaGenomeTextFile 12AromaGenomeTextFileDirectlyknownsubclasses:AromaUcscGenomeTextFilepublicabstractstaticclassAromaGenomeTextFileextendsFileCacheKeyInterfaceAnAromaGenomeTextFilerepresentsaannotationtabulartextlethatspeciesthenumberofbases(nucleotides)perchromosomeforaparticulargenome/organism.UsageAromaGenomeTextFile(...)Arguments...ArgumentspassedtoTabularTextFile.DetailsAnAromaGenomeTextFileisatab-delimitedtextlewithaheadercontaining(atleast)columnnames'chromosome'and'nbrOfBases'.The'chromosome'columnspeciesthechromosomes(characterstrings)andthe'nbrOfBases'columnspeciesthelengths(integer)ofthechromosomesinnumberofbases(nucleotides).ThelenameofanAromaGenomeTextFileshouldhaveformat&#xgeno;&#xme00;&#xtag0;"()andbelocatedin&#xgeno;&#xme00;annotationData/genomes/e.g.annotationData/genomes/Human/Human,chromosomes,max,20090503.txt.FieldsandMethodsMethods:byGenome-readDataFrame-MethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromTabularTextFile:as.character,getCommentChar,getDefaultColumnClassPatterns,getDefaultColumnClasses,getDe-faultColumnNames,getHeader,getReadArguments,hasColumnHeader,nbrOfLines,nbrOfRows,readColumnNames,readColumns,readDataFrame,readLines,readRawHeader,setCommentCharMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface: AromaGenomeTextFile13appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonExamples#LocateaHuman,chromosomes(,.*)*.txtfiledbAromaGenomeTextFile$byGenome("Human")print(db)#ReadthedatadfreadDataFrame(db)print(df)str(df)#Detailsonthefileformatooptsoptions(width=40)print(readLines(db))options(oopts) 14AromaMicroarrayDataFile AromaMicroarrayDataFileTheabstractAromaMicroarrayDataFileclass DescriptionPackage:aroma.coreClassAromaMicroarrayDataFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayDataFileDirectlyknownsubclasses:publicabstractstaticclassAromaMicroarrayDataFileextendsFileCacheKeyInterfaceAnAromaMicroarrayDataFileobjectrepresentsasinglemicroarraydatale.Eachsuchleorigi-natesfromaspecicchiptypeonagivenplatform.UsageAromaMicroarrayDataFile(...)Arguments...ArgumentspassedtoGenericDataFile.FieldsandMethodsMethods:getChipType-getPlatform-isAverageFile- AromaMicroarrayDataSet15MethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonSeeAlsoAnobjectofthisclassistypicallypartofanAromaMicroarrayDataSet. AromaMicroarrayDataSetTheAromaMicroarrayDataSetclass DescriptionPackage:aroma.coreClassAromaMicroarrayDataSetObject~~|~~+--FullNameInterface 16AromaMicroarrayDataSet~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--AromaMicroarrayDataSetDirectlyknownsubclasses:publicabstractstaticclassAromaMicroarrayDataSetextendsGenericDataFileSetAnAromaMicroarrayDataSetobjectrepresentsasetofAromaMicroarrayDataFileswithidenticalchiptypes.UsageAromaMicroarrayDataSet(files=NULL,...)ArgumentsfilesAlistofAromaMicroarrayDataFile:s....ArgumentspassedtoGenericDataFileSet.FieldsandMethodsMethods:as.AromaMicroarrayDataSetList-as.AromaMicroarrayDataSetTuple-getAverageFile-getChipType-getPlatform-MethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface: AromaMicroarrayDataSetTuple17appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaMicroarrayDataSetTupleTheAromaMicroarrayDataSetTupleclass DescriptionPackage:aroma.coreClassAromaMicroarrayDataSetTupleObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSetList~~~~~~~~~~~~|~~~~~~~~~~~~+--AromaMicroarrayDataSetTupleDirectlyknownsubclasses:AromaUnitTotalCnBinarySetTuplepublicabstractstaticclassAromaMicroarrayDataSetTupleextendsGenericDataFileSetListUsageAromaMicroarrayDataSetTuple(...,.setClass="AromaMicroarrayDataSet") 18AromaMicroarrayTabularBinaryFileArguments...ArgumentspassedtoGenericDataFileSetList..setClassThenameoftheclassoftheinputset.FieldsandMethodsMethods:as-as.AromaMicroarrayDataSetTuple-getChipTypes-getFullNames-getSets-getTags-nbrOfChipTypesGetsthenumberofchiptypes.MethodsinheritedfromGenericDataFileSetList:as,as.GenericDataFileSetList,as.character,as.data.frame,as.list,assertDuplicates,clone,extract,getAsteriskTags,getDefaultFullName,getFileList,getFileListClass,getFullNames,getNames,get-Set,getSets,getTags,indexOf,length,nbrOfFiles,nbrOfSets,setTagsMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaMicroarrayTabularBinaryFileTheAromaMicroarrayTabularBinaryFileclass AromaMicroarrayTabularBinaryFile19DescriptionPackage:aroma.coreClassAromaMicroarrayTabularBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayTabularBinaryFileDirectlyknownsubclasses:AromaCellCpgFile,AromaCellPositionFile,AromaCellSequenceFile,AromaCellTabularBinaryFile,AromaUFile,AromaUgcFile,AromaUgpFile,AromaUnitChromosomeTabularBinaryFile,Aro-maUnitGcContentFile,AromaUnitTabularBinaryFilepublicabstractstaticclassAromaMicroarrayTabularBinaryFileextendsAromaPlatformInterfaceAnAromaMicroarrayTabularBinaryFileisanabstractAromaTabularBinaryFile.UsageAromaMicroarrayTabularBinaryFile(...)Arguments...ArgumentspassedtoAromaTabularBinaryFile.FieldsandMethodsMethods:byChipType- 20AromaMicroarrayTabularBinaryFilegetChipType-getFilenameExtension-getPlatform-MethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach, AromaPlatform21equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonSeeAlsoAromaTabularBinaryFile. AromaPlatformTheAromaPlatformclass DescriptionPackage:aroma.coreClassAromaPlatformObject~~|~~+--AromaPlatformDirectlyknownsubclasses:publicabstractstaticclassAromaPlatformextendsObjectAnAromaPlatformprovidesmethodsforagivenplatform,e.g.Affymetrix,Agilent,Illumina.UsageAromaPlatform(...)Arguments...Notused.MethodsMethods:byName-equals-getAromaUgpFile- 22AromaPlatformInterfacegetName-getUnitNamesFile-getUnitTypesFile-MethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonExamples##Notrun:library("aroma.affymetrix")platformAromaPlatform$byName("Affymetrix")print(platform)stopifnot(getName(platform)=="Affymetrix")##End(Notrun) AromaPlatformInterfaceTheAromaPlatformInterfaceclass DescriptionPackage:aroma.coreClassAromaPlatformInterfaceInterface~~|~~+--AromaPlatformInterfaceDirectlyknownsubclasses:AromaCellCpgFile,AromaCellPositionFile,AromaCellSequenceFile,AromaCellTabularBinaryFile,AromaMicroarrayTabularBinaryFile,AromaUFile,AromaUgcFile,AromaUgpFile,AromaUnit-CallFile,AromaUnitChromosomeTabularBinaryFile,AromaUnitFracBCnBinaryFile,AromaUnit-GcContentFile,AromaUnitGenotypeCallFile,AromaUnitPscnBinaryFile,AromaUnitSignalBina-ryFile,AromaUnitTabularBinaryFile,AromaUnitTotalCnBinaryFile,AromaUnitTypesFile AromaRepository23publicabstractclassAromaPlatformInterfaceextendsInterfaceAnAromaPlatformInterfaceprovidesmethodsforagivenplatform,e.g.Affymetrix,Agilent,Illu-mina.UsageAromaPlatformInterface(...)Arguments...Notused.MethodsMethods:getAromaPlatformGetstheplatform.getAromaUflFile-getAromaUgpFile-getChipTypeGetsthechiptype.getPlatformGetstheplatform.getUnitNamesFile-getUnitTypesFile-MethodsinheritedfromInterface:extend,print,usesAuthor(s)HenrikBengtsson AromaRepositoryTheAromaRepositoryclass DescriptionPackage:aroma.coreClassAromaRepositoryObject~~|~~+--AromaRepository 24AromaRepositoryDirectlyknownsubclasses:publicstaticclassAromaRepositoryextendsObjectAnAromaRepositoryobjectprovidesmethodsfordownloadingannotationdatafromtheAromarepository.UsageAromaRepository(urlPath="https://www.aroma-project.org/data",verbose=FALSE,...)ArgumentsurlPathTheURLtotheAromarepository.verboseTheVerbosetobeusedduringprocessing....Notused.MethodsMethods:downloadACC-downloadACM-downloadACP-downloadACS-downloadAll-downloadCDF-downloadChipTypeFileDownloadaparticularchiptypeannotationle.downloadProbeSeqsTXT-downloadTXT-downloadUFL-downloadUGC-downloadUGP-MethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaTabularBinaryFile25 AromaTabularBinaryFileTheAromaTabularBinaryFileclass DescriptionPackage:aroma.coreClassAromaTabularBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFileDirectlyknownsubclasses:AromaCellCpgFile,AromaCellPositionFile,AromaCellSequenceFile,AromaCellTabularBinaryFile,AromaMicroarrayTabularBinaryFile,AromaUFile,AromaUgcFile,AromaUgpFile,AromaUnit-CallFile,AromaUnitChromosomeTabularBinaryFile,AromaUnitFracBCnBinaryFile,AromaUnit-GcContentFile,AromaUnitGenotypeCallFile,AromaUnitPscnBinaryFile,AromaUnitSignalBina-ryFile,AromaUnitTabularBinaryFile,AromaUnitTotalCnBinaryFile,AromaUnitTypesFilepublicabstractstaticclassAromaTabularBinaryFileextendsFileCacheKeyInterfaceAAromaTabularBinaryFilerepresentsalewithabinaryformat.Ithasawelldenedheader,adatasection,andafooter.UsageAromaTabularBinaryFile(...)Arguments...ArgumentspassedtoGenericTabularFile. 26AromaTabularBinaryFileFieldsandMethodsMethods:[-[-colMeans-colSums-getBytesPerColumn-getColClasses-importFrom-nbrOfColumns-nbrOfRows-readColumns-readFooterReadsthelefooterinXMLformatintoanamednestedlist.subset-summary-writeFooterWritesanamednestedlisttothelefooterinXMLformat.MethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull- AromaTabularBinarySet27NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonSeeAlsoGenericDataFile. AromaTabularBinarySetTheAromaTabularBinarySetclass DescriptionPackage:aroma.coreClassAromaTabularBinarySetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySetDirectlyknownsubclasses:AromaUnitCallSet,AromaUnitFracBCnBinarySet,AromaUnitGenotypeCallSet,AromaUnitPscn-BinarySet,AromaUnitSignalBinarySet,AromaUnitTotalCnBinarySetpublicstaticclassAromaTabularBinarySetextendsGenericTabularFileSetAnAromaTabularBinarySetobjectrepresentsasetofAromaTabularBinaryFileswithidenticalchiptypes. 28AromaTabularBinarySetUsageAromaTabularBinarySet(files=NULL,...)ArgumentsfilesAlistofAromaTabularBinaryFile:s....ArgumentspassedtoGenericDataFileSet.FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaTransform29 AromaTransformTheAromaTransformclass DescriptionPackage:aroma.coreClassAromaTransformObject~~|~~+--ParametersInterface~~~~~~~|~~~~~~~+--AromaTransformDirectlyknownsubclasses:publicabstractstaticclassAromaTransformextendsParametersInterfaceThisabstractclassrepresentsatransform(algorithm/operator)thattransformsdata.Atransformhasaninputdataset,whichistransformedintoanoutputdataset.UsageAromaTransform(dataSet=NULL,tags="*",...,.reqSetClass="AromaMicroarrayDataSet")ArgumentsdataSetTheinputdatasetasanAromaMicroarrayDataSet.tagsAcharactervectoroftagstobeappendedtothetagsoftheinputdataset....Notused..reqSetClassInternalargument.DetailsSubclassesmustimplementtheprocess()method.FieldsandMethodsMethods:getFullNameGetsthefullnameoftheoutputdataset.getInputDataSetGetstheinputdataset. 30AromaUnitCallFilegetNameGetsthenameoftheoutputdataset.getOutputDataSetGetsthetransformeddataset.getPathGetsthepathoftheoutputdirectory.getRootPathGetstherootpathoftheoutputdirectory.getTagsGetsthetagsoftheoutputdataset.isDoneChecksifthedatasetisprocessedornot.processProcessesthedataset.setTags-MethodsinheritedfromParametersInterface:getParameterSets,getParameters,getParametersAsStringMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitCallFileTheAromaUnitCallFileclass DescriptionPackage:aroma.coreClassAromaUnitCallFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface AromaUnitCallFile31~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallFileDirectlyknownsubclasses:AromaUnitGenotypeCallFilepublicstaticclassAromaUnitCallFileextendsAromaUnitSignalBinaryFileAnAromaUnitCallFileisaAromaUnitSignalBinaryFile.UsageAromaUnitCallFile(...)Arguments...ArgumentspassedtoAromaUnitSignalBinaryFile.FieldsandMethodsMethods:extractCallArray-extractCalls-extractMatrix-findUnitsTodo-MethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrameMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKey 32AromaUnitCallSetMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitCallSetTheAromaUnitCallSetclass DescriptionPackage:aroma.coreClassAromaUnitCallSet AromaUnitCallSet33Object~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallSetDirectlyknownsubclasses:AromaUnitGenotypeCallSetpublicstaticclassAromaUnitCallSetextendsAromaUnitSignalBinarySetAnAromaUnitCallSetobjectrepresentsasetofAromaUnitCallFileswithidenticalchiptypes.UsageAromaUnitCallSet(...)Arguments...ArgumentspassedtoAromaUnitSignalBinarySet.FieldsandMethodsMethods:extractCallArray-extractCalls-extractGenotypeMatrix-findUnitsTodo-MethodsinheritedfromAromaUnitSignalBinarySet:byName,ndByName,getAromaFullNameTranslatorSet,getAromaUgpFile,getChipType,getPlat-form,validate,writeDataFrameMethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTags 34AromaUnitFracBCnBinaryFileMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitFracBCnBinaryFileTheAromaUnitFracBCnBinaryFileclass DescriptionPackage:aroma.coreClassAromaUnitFracBCnBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface AromaUnitFracBCnBinaryFile35~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitFracBCnBinaryFileDirectlyknownsubclasses:publicstaticclassAromaUnitFracBCnBinaryFileextendsAromaUnitSignalBinaryFileAnAromaUnitFracBCnBinaryFileisaAromaUnitTabularBinaryFile.UsageAromaUnitFracBCnBinaryFile(...)Arguments...ArgumentspassedtoAromaUnitTabularBinaryFile.FieldsandMethodsMethods:extractRawAlleleBFractions-MethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrameMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWith 36AromaUnitFracBCnBinaryFileMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitFracBCnBinarySet37 AromaUnitFracBCnBinarySetTheAromaUnitFracBCnBinarySetclass DescriptionPackage:aroma.coreClassAromaUnitFracBCnBinarySetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitFracBCnBinarySetDirectlyknownsubclasses:publicstaticclassAromaUnitFracBCnBinarySetextendsAromaUnitSignalBinarySetAnAromaUnitFracBCnBinarySetobjectrepresentsasetofAromaUnitFracBCnBinaryFileswithidenticalchiptypes.UsageAromaUnitFracBCnBinarySet(...)Arguments...ArgumentspassedtoAromaUnitSignalBinarySet.DetailsTheterm"alleleBfraction"isalsoknowas"alleleBfrequency",whichwascoinedbyPeifferetal.(2006).Notethattheterm"frequency"isabitmisleadingsinceitisnotafrequencyinneitherthestatisticalnorthepopulationsense,butratheronlyproportionrelativetothetotalamountofalleleAandalleleBsignals,whichiscalculatedforeachsampleindependently. 38AromaUnitFracBCnBinarySetFieldsandMethodsMethods:byName-writeDataFrame-MethodsinheritedfromAromaUnitSignalBinarySet:byName,ndByName,getAromaFullNameTranslatorSet,getAromaUgpFile,getChipType,getPlat-form,validate,writeDataFrameMethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTagsMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitGenotypeCallFile39References[1]Peifferetal.,High-resolutiongenomicprolingofchromosomalaberrationsusingInniumwhole-genomegenotyping,GenomeRes,2006. AromaUnitGenotypeCallFileTheAromaUnitGenotypeCallFileclass DescriptionPackage:aroma.coreClassAromaUnitGenotypeCallFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitGenotypeCallFileDirectlyknownsubclasses:publicstaticclassAromaUnitGenotypeCallFileextendsAromaUnitCallFileAnAromaUnitGenotypeCallFileisaAromaUnitTabularBinaryFile. 40AromaUnitGenotypeCallFileUsageAromaUnitGenotypeCallFile(...)Arguments...ArgumentspassedtoAromaUnitTabularBinaryFile.FieldsandMethodsMethods:extractGenotypeMatrix-extractGenotypes-isHeterozygous-isHomozygous-updateGenotypes-MethodsinheritedfromAromaUnitCallFile:allocate,extractCallArray,extractCalls,extractMatrix,ndUnitsTodoMethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrameMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames, AromaUnitGenotypeCallSet41getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitGenotypeCallSetTheAromaUnitGenotypeCallSetclass DescriptionPackage:aroma.coreClassAromaUnitGenotypeCallSetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet 42AromaUnitGenotypeCallSet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitCallSet~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitGenotypeCallSetDirectlyknownsubclasses:publicstaticclassAromaUnitGenotypeCallSetextendsAromaUnitCallSetAnAromaUnitGenotypeCallSetobjectrepresentsasetofAromaUnitGenotypeCallFileswithidenticalchiptypes.UsageAromaUnitGenotypeCallSet(...)Arguments...ArgumentspassedtoAromaUnitCallSet.FieldsandMethodsMethods:byName-extractGenotypes-MethodsinheritedfromAromaUnitCallSet:byPath,extractCallArray,extractCalls,extractGenotypeMatrix,ndByName,ndUnitsTodoMethodsinheritedfromAromaUnitSignalBinarySet:byName,ndByName,getAromaFullNameTranslatorSet,getAromaUgpFile,getChipType,getPlat-form,validate,writeDataFrameMethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTagsMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy- AromaUnitPscnBinaryFile43function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitPscnBinaryFileTheAromaUnitPscnBinaryFileclass DescriptionPackage:aroma.coreClassAromaUnitPscnBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface 44AromaUnitPscnBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitPscnBinaryFileDirectlyknownsubclasses:publicabstractstaticclassAromaUnitPscnBinaryFileextendsCopyNumberDataFileAnAromaUnitPscnBinaryFileisaAromaUnitSignalBinaryFilethatholdstotalcopynumbersignals(TCNs)andalleleBfractions(BAFs).TheTCNscaneitherbeonanunknownscaleorratiosrelativetoareference.Thesignalsarealwaysstoredontheoriginalscale,i.e.theyareneverstoredonthelogaritmicscale.TheBAFsarealwaysona[0-eps,1+eps]scale,whereeps�=0.UsageAromaUnitPscnBinaryFile(...)Arguments...ArgumentspassedtoAromaUnitSignalBinaryFile.FieldsandMethodsMethods:extractRawCopyNumbers-hasAlleleBFractions-hasStrandiness-hasTotalCopyNumberRatios-MethodsinheritedfromCopyNumberDataFile:as,as.CopyNumberDataFile,getNumberOfFilesAveraged,hasAlleleBFractions,hasStrandinessMethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrame AromaUnitPscnBinaryFile45MethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson 46AromaUnitPscnBinarySet AromaUnitPscnBinarySetTheAromaUnitPscnBinarySetclass DescriptionPackage:aroma.coreClassAromaUnitPscnBinarySetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataSet~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitPscnBinarySetDirectlyknownsubclasses:publicstaticclassAromaUnitPscnBinarySetextendsCopyNumberDataSetAnAromaUnitPscnBinarySetobjectrepresentsasetofAromaUnitPscnBinaryFileswithidenticalchiptypes.UsageAromaUnitPscnBinarySet(...)Arguments...ArgumentspassedtoAromaUnitSignalBinarySet.FieldsandMethodsMethods: AromaUnitPscnBinarySet47byName-getAverageFile-writeDataFrame-MethodsinheritedfromCopyNumberDataSet:as,as.CopyNumberDataSet,doCBS,hasAlleleBFractions,hasStrandinessMethodsinheritedfromAromaUnitSignalBinarySet:byName,ndByName,getAromaFullNameTranslatorSet,getAromaUgpFile,getChipType,getPlat-form,validate,writeDataFrameMethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTagsMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson 48AromaUnitSignalBinaryFile AromaUnitSignalBinaryFileTheAromaUnitSignalBinaryFileclass DescriptionPackage:aroma.coreClassAromaUnitSignalBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFileDirectlyknownsubclasses:AromaUnitCallFile,AromaUnitFracBCnBinaryFile,AromaUnitGenotypeCallFile,AromaUnitPsc-nBinaryFile,AromaUnitTotalCnBinaryFile,AromaUnitTypesFilepublicstaticclassAromaUnitSignalBinaryFileextendsAromaPlatformInterfaceAnAromaUnitSignalBinaryFileisaAromaTabularBinaryFile.UsageAromaUnitSignalBinaryFile(...)Arguments...ArgumentspassedtoAromaTabularBinaryFile. AromaUnitSignalBinaryFile49FieldsandMethodsMethods:extractMatrix-getChipType-getNumberOfFilesAveraged-getPlatform-isAverageFile-nbrOfUnits-readDataFrame-writeDataFrameWritesthedataleasatab-delimitedtextle.MethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab- 50AromaUnitSignalBinarySetularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonSeeAlsoAromaTabularBinaryFile. AromaUnitSignalBinarySetTheAromaUnitSignalBinarySetclass DescriptionPackage:aroma.coreClassAromaUnitSignalBinarySetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySetDirectlyknownsubclasses:AromaUnitCallSet,AromaUnitFracBCnBinarySet,AromaUnitGenotypeCallSet,AromaUnitPscn-BinarySet,AromaUnitTotalCnBinarySetpublicstaticclassAromaUnitSignalBinarySetextendsAromaTabularBinarySet AromaUnitSignalBinarySet51AnAromaUnitSignalBinarySetobjectrepresentsasetofAromaUnitSignalBinaryFileswithiden-ticalchiptypes.UsageAromaUnitSignalBinarySet(...)Arguments...ArgumentspassedtoAromaTabularBinarySet.FieldsandMethodsMethods:byName-getAromaUgpFile-getChipType-getPlatform-writeDataFrameWritesthedatasetasatab-delimitedtextle.MethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTagsMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject: 52AromaUnitTabularBinaryFile$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitTabularBinaryFileTheAromaUnitTabularBinaryFileclass DescriptionPackage:aroma.coreClassAromaUnitTabularBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaMicroarrayTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTabularBinaryFileDirectlyknownsubclasses:AromaUFile,AromaUgcFile,AromaUgpFile,AromaUnitChromosomeTabularBinaryFile,Aro-maUnitGcContentFile AromaUnitTabularBinaryFile53publicabstractstaticclassAromaUnitTabularBinaryFileextendsUnitAnnotationDataFileAAromaUnitTabularBinaryFileisanAromaTabularBinaryFilewiththeconstraintthattherowsmapone-to-oneto,andinthesameorderas,theunitsinaannotationchiptypele(e.g.CDFle).The(full)chiptypeoftheannotationchiptypeleisgivenbythemandatorylefooterchipType.UsageAromaUnitTabularBinaryFile(...)Arguments...ArgumentspassedtoAromaTabularBinaryFile.FieldsandMethodsMethods:byChipType-nbrOfUnits-writeDataFrameWritesthedataleasatab-delimitedtextle.MethodsinheritedfromUnitAnnotationDataFile:byChipType,getAromaUFile,getAromaUgpFile,getChipType,getDefaultExtension,getPlatform,nbrOfUnitsMethodsinheritedfromAromaMicroarrayTabularBinaryFile:allocate,as.character,byChipType,ndByChipType,getChipType,getFilenameExtension,getPlat-formMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFiles 54AromaUnitTotalCnBinaryFileMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitTotalCnBinaryFileTheAromaUnitTotalCnBinaryFileclass DescriptionPackage:aroma.coreClassAromaUnitTotalCnBinaryFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile AromaUnitTotalCnBinaryFile55~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTotalCnBinaryFileDirectlyknownsubclasses:publicabstractstaticclassAromaUnitTotalCnBinaryFileextendsCopyNumberDataFileAnAromaUnitTotalCnBinaryFileisaAromaUnitSignalBinaryFile.UsageAromaUnitTotalCnBinaryFile(...)Arguments...ArgumentspassedtoAromaUnitSignalBinaryFile.FieldsandMethodsMethods:extractPSCNArray-extractPSCNMatrix-extractRawCopyNumbers-getAM-hasAlleleBFractions-hasStrandiness- 56AromaUnitTotalCnBinaryFileMethodsinheritedfromCopyNumberDataFile:as,as.CopyNumberDataFile,getNumberOfFilesAveraged,hasAlleleBFractions,hasStrandinessMethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrameMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKeyMethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullName AromaUnitTotalCnBinarySet57MethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitTotalCnBinarySetTheAromaUnitTotalCnBinarySetclass DescriptionPackage:aroma.coreClassAromaUnitTotalCnBinarySetObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFileSet~~~~~~~~~~~~|~~~~~~~~~~~~+--GenericTabularFileSet~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataSet~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTotalCnBinarySetDirectlyknownsubclasses:publicstaticclassAromaUnitTotalCnBinarySetextendsCopyNumberDataSetAnAromaUnitTotalCnBinarySetobjectrepresentsasetofAromaUnitTotalCnBinaryFileswithidenticalchiptypes.UsageAromaUnitTotalCnBinarySet(...) 58AromaUnitTotalCnBinarySetArguments...ArgumentspassedtoAromaUnitSignalBinarySet.FieldsandMethodsMethods:as.AromaUnitTotalCnBinarySetTuple-as.CopyNumberDataSetTuple-byName-exportAromaUnitPscnBinarySet-exportTotalCnRatioSet-extractPSCNArray-getAverageFile-getUnitNamesFile-writeDataFrame-MethodsinheritedfromCopyNumberDataSet:as,as.CopyNumberDataSet,doCBS,hasAlleleBFractions,hasStrandinessMethodsinheritedfromAromaUnitSignalBinarySet:byName,ndByName,getAromaFullNameTranslatorSet,getAromaUgpFile,getChipType,getPlat-form,validate,writeDataFrameMethodsinheritedfromAromaTabularBinarySet:getDefaultFullName,getRootName,setAttributesBy,setAttributesBySampleAnnotationFile,setAt-tributesBySampleAnnotationSet,setAttributesByTagsMethodsinheritedfromGenericTabularFileSet:extractMatrix,calculateAverageColumnAcrossFilesMethodsinheritedfromGenericDataFileSet:[,[[,anyDuplicated,anyNA,append,appendFiles,appendFullNamesTranslator,appendFullNames-TranslatorByNULL,appendFullNamesTranslatorByTabularTextFile,appendFullNamesTranslator-ByTabularTextFileSet,appendFullNamesTranslatorBydata.frame,appendFullNamesTranslatorBy-function,appendFullNamesTranslatorBylist,as.character,as.list,byName,byPath,c,clearCache,clearFullNamesTranslator,clone,copyTo,dsApply,dsApplyInPairs,duplicated,equals,extract,ndByName,ndDuplicated,getChecksum,getChecksumFileSet,getChecksumObjects,getDe-faultFullName,getFile,getFileClass,getFileSize,getFiles,getFullNames,getNames,getOneFile,getPath,getPathnames,getSubdirs,gunzip,gzip,hasFile,indexOf,is.na,names,nbrOfFiles,rep,resetFullNames,setFullNamesTranslator,sortBy,unique,update2,updateFullName,updateFull-Names,validate,getFullNameTranslatorSet,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags, AromaUnitTypesFile59hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson AromaUnitTypesFileTheAromaUnitTypesFileclass DescriptionPackage:aroma.coreClassAromaUnitTypesFileObject~~|~~+--FullNameInterface~~~~~~~|~~~~~~~+--GenericDataFile~~~~~~~~~~~~|~~~~~~~~~~~~+--ColumnNamesInterface~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GenericTabularFile~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitAnnotationDataFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--UnitTypesFile~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTypesFile 60AromaUnitTypesFileDirectlyknownsubclasses:publicstaticclassAromaUnitTypesFileextendsUnitTypesFileUsageAromaUnitTypesFile(...)Arguments...ArgumentspassedtoAromaUnitTabularBinaryFile.FieldsandMethodsMethods:getChipType-getPlatform-getUnitTypes-importFromUnitTypesFile-MethodsinheritedfromUnitTypesFile:getUnitTypes,nbrOfUnitsMethodsinheritedfromUnitAnnotationDataFile:byChipType,getAromaUFile,getAromaUgpFile,getChipType,getDefaultExtension,getPlatform,nbrOfUnitsMethodsinheritedfromAromaUnitSignalBinaryFile:allocate,allocateFromUnitAnnotationDataFile,allocateFromUnitNamesFile,as.character,extract-Matrix,extractRawGenomicSignals,fromFile,getChipType,getExtensionPattern,getFilenameEx-tension,getNumberOfFilesAveraged,getPlatform,isAverageFile,nbrOfUnits,readDataFrame,write-DataFrameMethodsinheritedfromAromaPlatformInterface:getAromaPlatform,getAromaUFile,getAromaUgpFile,getChipType,getPlatform,getUnitAnno-tationDataFile,getUnitNamesFile,getUnitTypesFile,isCompatibleWithMethodsinheritedfromAromaTabularBinaryFile:[,[[[,allocate,as.character,colApply,colMeans,colStats,colSums,dimnamesgetBytes-PerColumn,getColClasses,getDefaultColumnNames,getRootName,importFrom,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,readFooter,readHeader,readRawFooter,setAttributes-ByTags,subset,summary,updateData,updateDataColumn,writeFooter,writeRawFooterMethodsinheritedfromFileCacheKeyInterface:getCacheKey BinnedScatter61MethodsinheritedfromCacheKeyInterface:getCacheKeyMethodsinheritedfromGenericTabularFile:[,as.character,dim,extractMatrix,head,nbrOfColumns,nbrOfRows,readColumns,readDataFrame,tail,writeColumnsToFilesMethodsinheritedfromColumnNamesInterface:appendColumnNamesTranslator,appendColumnNamesTranslatorByNULL,appendColumnNames-TranslatorBycharacter,appendColumnNamesTranslatorByfunction,appendColumnNamesTransla-torBylist,clearColumnNamesTranslator,clearListOfColumnNamesTranslators,getColumnNames,getColumnNamesTranslator,getDefaultColumnNames,getListOfColumnNamesTranslators,nbrOf-Columns,setColumnNames,setColumnNamesTranslator,setListOfColumnNamesTranslators,up-dateColumnNamesMethodsinheritedfromGenericDataFile:as.character,clone,compareChecksum,copyTo,equals,fromFile,getAttribute,getAttributes,getCheck-sum,getChecksumFile,getCreatedOn,getDefaultFullName,getExtension,getExtensionPattern,getFileSize,getFileType,getFilename,getFilenameExtension,getLastAccessedOn,getLastModi-edOn,getOutputExtension,getPath,getPathname,gunzip,gzip,hasBeenModied,is.na,isFile,isGzipped,linkTo,readChecksum,renameTo,renameToUpperCaseExt,setAttribute,setAttributes,setAttributesBy,setAttributesByTags,setExtensionPattern,testAttributes,validate,validateCheck-sum,writeChecksum,getParentNameMethodsinheritedfromFullNameInterface:appendFullNameTranslator,appendFullNameTranslatorByNULL,appendFullNameTranslatorByTab-ularTextFile,appendFullNameTranslatorByTabularTextFileSet,appendFullNameTranslatorBychar-acter,appendFullNameTranslatorBydata.frame,appendFullNameTranslatorByfunction,appendFull-NameTranslatorBylist,clearFullNameTranslator,clearListOfFullNameTranslators,getDefaultFull-Name,getFullName,getFullNameTranslator,getListOfFullNameTranslators,getName,getTags,hasTag,hasTags,resetFullName,setFullName,setFullNameTranslator,setListOfFullNameTrans-lators,setName,setTags,updateFullNameMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson BinnedScatterTheBinnedScatterclass DescriptionPackage:aroma.coreClassBinnedScatter 62BinnedScatterlist~~|~~+--BinnedScatterDirectlyknownsubclasses:publicclassBinnedScatterextendslistUsageBinnedScatter(data=NULL,density=NULL,map=NULL,params=NULL)ArgumentsdataANx2numericmatrix.density...map...paramsAlistofparameters.FieldsandMethodsMethods:plot-points-reorder-subsample-subset-Methodsinheritedfromlist:Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,all.equal,as.CopyNumberDataSetTuple,as.data.frame,attachLocally,callHooks,coerce,ANY,list-method,exportAromaUnitPscnBinarySet,listToXml,mergeBoxplotStats,relist,type.convert,withinAuthor(s)HenrikBengtssonSeeAlsoThespatialdensityisestimatedbyinternalfunctionsofthesmoothScatterpackage. CbsModel63Examples#Samplescatterdatan10e3xrnorm(n=n)yrnorm(n=n)xycbind(x=x,y=sin(x)+y/5)#BindataandestimatedensitiesxydbinScatter(xy)layout(matrix(1:4,nrow=2))par(mar=c(5,4,2,1))#Plotdataplot(xyd,pch=1)#Thinscatterdatabysubsamplingrhosc(1/3,1/4,1/6)for(kkinseq_along(rhos)){xyd2subsample(xyd,size=rhos[kk])points(xyd2,pch=1,col=kk+1)}for(kkinseq_along(rhos)){xyd2subsample(xyd,size=rhos[kk])plot(xyd2,pch=1,col=kk+1)mtext(side=3,line=0,sprintf("Density:%.1f%%",100*rhos[kk]))} CbsModelTheCbsModelclass DescriptionPackage:aroma.coreClassCbsModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModel~~~~~~~~~~~~|~~~~~~~~~~~~+--CopyNumberSegmentationModel~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--CbsModel 64CbsModelDirectlyknownsubclasses:publicstaticclassCbsModelextendsCopyNumberSegmentationModelThisclassrepresentstheCircularBinarySegmentation(CBS)model[1].UsageCbsModel(cesTuple=NULL,...,seed=NULL)ArgumentscesTupleACopyNumberDataSetTuple....ArgumentspassedtotheconstructorofCopyNumberSegmentationModel.seedAn(optional)integerthatifspeciedwill(temporarily)settherandomseedeachtimebeforecallingthesegmentationmethod.Formoreinformation,seesegmentByCBS().FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromCopyNumberSegmentationModel:t,getAsteriskTags,getFitFunction,getFullNames,getRegions,getTags,plot,plotCopyNumber-RegionLayers,writeRegionsMethodsinheritedfromCopyNumberChromosomalModel:as.character,calculateChromosomeStatistics,calculateRatios,estimateSds,extractRawCopyNum-bers,t,getChromosomeLength,getDataFileMatrix,getMaxNAFraction,getNames,getOption-alArguments,getPairedNames,getRefSetTuple,getReference,getReferenceSetTuple,isPaired,new-Plot,plotAxesLayers,plotChromosomesLayers,plotCytobandLayers,plotFitLayers,plotGridHor-izontalLayers,plotRawCopyNumbers,plotSampleLayers,setReferenceMethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson ChromosomalModel65References[1]Olshen,A.B.,Venkatraman,E.S.,Lucito,R.,Wigler,M.Circularbinarysegmentationfortheanalysisofarray-basedDNAcopynumberdata.Biostatistics5:557-572,2004.[2]Venkatraman,E.S.&Olshen,A.B.AfastercircularbinarysegmentationalgorithmfortheanalysisofarrayCGHdata.Bioinformatics,2007.SeeAlsoCopyNumberSegmentationModel. ChromosomalModelTheChromosomalModelclass DescriptionPackage:aroma.coreClassChromosomalModelObject~~|~~+--ChromosomalModelDirectlyknownsubclasses:CbsModel,CopyNumberChromosomalModel,CopyNumberSegmentationModel,GladModel,HaarSeg-Model,RawCopyNumberModelpublicabstractstaticclassChromosomalModelextendsObjectThisabstractclassrepresentsachromosomalmodel.UsageChromosomalModel(cesTuple=NULL,tags="*",genome="Human",chromosomes=NULL,...)ArgumentscesTupleAAromaMicroarrayDataSetTuple.tagsAcharactervectoroftags.genomeAcharacterstringspecifyingwhatgenomeisprocess.chromosomes(optional)Avectorspecifyingwhichchromosomestoprocess....Notused. 66ChromosomeExplorerFieldsandMethodsMethods:fit-getChipTypeGetsalabelforallchiptypesmerged.getChipTypes-getChromosomesGetsthechromosomestobeprocessed.getFullName-getFullNames-getGenome-getName-getNamesGetsthenamesofthearrays.getPath-getSets-getTags-indexOf-nbrOfArraysGetsthenumberofarrays.nbrOfChipTypesGetsthenumberofchiptypes.setChromosomes-setGenome-MethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisRequirementsThisclassrequiresgenomeinformationannotationlesforeverychiptype.Author(s)HenrikBengtsson ChromosomeExplorerTheChromosomeExplorerclass DescriptionPackage:aroma.coreClassChromosomeExplorerObject~~| ChromosomeExplorer67~~+--Explorer~~~~~~~|~~~~~~~+--ChromosomeExplorerDirectlyknownsubclasses:publicstaticclassChromosomeExplorerextendsExplorerUsageChromosomeExplorer(model=NULL,zooms=2^(0:6),...)ArgumentsmodelACopyNumberChromosomalModelobject.zoomsAnpositiveintegervectorspecifyingforwhichzoomlevelsthegraphicsshouldbegenerated....Notused.FieldsandMethodsMethods:display-getChromosomesGetsthechromosomesavailable.getFullNames-getModelGetsthemodel.getNames-getPath-getZooms-indexOf-processGeneratesimageles,scriptsanddynamicpagesfortheexplorer.setArraysSetsthearrays.setCytoband-setZooms-MethodsinheritedfromExplorer:addIncludes,addIndexFile,as.character,display,getAlias,getArraysOfInput,getAsteriskTags,get-FullName,getIncludePath,getMainPath,getName,getNameOfInput,getNames,getPath,getRe-portPathPattern,getRootPath,getSampleLayerPrex,getSubname,getTags,getTagsOfInput,get-TemplatePath,getVersion,nbrOfArrays,process,setAlias,setArrays,setReportPathPattern,set-Subname,setup,splitByReportPathPattern,updateSetupExplorerFileMethodsinheritedfromObject: 68colBinnedSmoothing.matrix$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisGeneratingPNGimagesInordertogetbetterlookinggraphs,butalsotobeabletogeneratebitmapimagesonsystemswith-outdirectbitmapsupport,whichisthecasewhenrunningRinbatchmodeoronUnixwithoutX11support,imagesarecreatedusingthepng2device(awrapperforbitmap()imitatingpng()).Thepng()isonlyusedifpng2(),whichrequiresGhostscript,doesnot.Note,whenimagesarecreatedusingpng2(),theimagesdoesnotappearimmediately,althoughthefunctioncalliscompleted,sobepatient.Author(s)HenrikBengtssonSeeAlsoCopyNumberChromosomalModel. colBinnedSmoothing.matrixBinnedsmoothingofamatrixcolumnbycolumn DescriptionBinnedsmoothingofamatrixcolumnbycolumn.Usage##S3methodforclass'matrix'colBinnedSmoothing(Y,x=seq_len(nrow(Y)),w=NULL,xOut=NULL,xOutRange=NULL,from=min(x,na.rm=TRUE),to=max(x,na.rm=TRUE),by=NULL,length.out=length(x),na.rm=TRUE,FUN="median",...,verbose=FALSE)ArgumentsYAnumericJxImatrix(oravectoroflengthJ.)xA(optional)numericvectorspecifyingthepositionsoftheJentries.Thedefaultistoassumeuniformlydistributedpositions.wAoptionalnumericvectorofpriorweightsforeachoftheJentries.xOutOptionalnumericvectorofKbincenterlocations.xOutRangeOptionalKx2matrixspecifyingtheboundarylocationsforKbins,whereeachrowrepresentsabin[x0;x1).Ifnotspecied,theboundariesaresettobethemidpointsofthebincenters,suchthatthebinshavemaximumlengthswithoutoverlapping.Viceverse,ifxOutisnotspecied,thenxOutissettobethemidpointsofthexOutRangeboundaries. colBinnedSmoothing.matrix69from,to,by,length.outIfneitherxOutnorxOutRangeisspecied,thexOutisgenerateduniformlyfromthesearguments,whichspecifythecenterlocationoftherstandthelastbin,andthedistancebetweenthecenterlocations,utilizingtheseq()function.Argumentlength.outcanbeusedasanalternativetoby,incaseitspeciesthetotalnumberofbinsinstead.FUNAfunction.na.rmIfTRUE,missingvaluesareexcluded,otherwisenot....Notused.verboseSeeVerbose.DetailsNotethatallzero-lengthbins[x0;x1)willgetresultinanNAvalue,becausesuchbinscontainnodatapoints.ThisalsomeansthatcolBinnedSmoothing(Y,x=x,xOut=xOut)wherexOutcontainsduplicatedvalues,willresultinsomezero-lengthbinsandhenceNAvalues.ValueReturnsanumericKxImatrix(oravectoroflengthK)whereKisthetotalnumberofbins.Thefollowingattributesarealsoreturned:•xOutThecenterlocationsofeachbin.•xOutRangeThebinboundaries.•countThenumberofdatapointswithineachbin(basedsolelyonargumentx).•binWidthTheaveragebinwidth.Author(s)HenrikBengtssonSeeAlso*colKernelSmoothing().Examples#NumberoftracksI4#NumberofdatapointspertrackJ100#Simulatedatawithagainintrack2and3x1:JYmatrix(rnorm(I*J,sd=1/2),ncol=I)Y[30:50,2:3]Y[30:50,2:3]+3#Uniformlydistributedequal-sizedbins 70colBinnedSmoothing.matrixYs3colBinnedSmoothing(Y,x=x,from=2,by=3)Ys5colBinnedSmoothing(Y,x=x,from=3,by=5)#CustombinsxOutRanget(matrix(c(1,11,11,31,31,41,41,51,51,81,81,91,91,101),nrow=2))YsCcolBinnedSmoothing(Y,x=x,xOutRange=xOutRange)#Custombinsspecifiedbycenterlocationswith#maximizedwidthrelativetotheneighboringbins.xOutc(6,21,36,46,66,86,96)YsDcolBinnedSmoothing(Y,x=x,xOut=xOut)xlimrange(x)ylimc(-3,5)layout(matrix(1:I,ncol=1))par(mar=c(3,3,1,1)+0.1,pch=19)for(iiin1:I){plot(NA,xlim=xlim,ylim=ylim)points(x,Y[,ii],col="#999999")xOutattr(Ys3,"xOut")lines(xOut,Ys3[,ii],col=2)points(xOut,Ys3[,ii],col=2)xOutattr(Ys5,"xOut")lines(xOut,Ys5[,ii],col=3)points(xOut,Ys5[,ii],col=3)xOutattr(YsC,"xOut")lines(xOut,YsC[,ii],col=4)points(xOut,YsC[,ii],col=4,pch=15)xOutattr(YsD,"xOut")lines(xOut,YsD[,ii],col=5)points(xOut,YsD[,ii],col=5,pch=15)if(ii==1){legend("topright",pch=c(19,19,15,15),col=c(2,3,4,5),c("by=3","by=5","Custom#1","Custom#2"),horiz=TRUE,bty="n")}}#SanitychecksxOutx colKernelSmoothing.matrix71YsTcolBinnedSmoothing(Y,x=x,xOut=xOut)stopifnot(all(YsT==Y))stopifnot(all(attr(YsT,"counts")==1))xOutattr(YsD,"xOut")YsEcolBinnedSmoothing(YsD,x=xOut,xOut=xOut)stopifnot(all(YsE==YsD))stopifnot(all(attr(YsE,"xOutRange")==attr(YsD,"xOutRange")))stopifnot(all(attr(YsE,"counts")==1))#Scrambleorderingoflociidxssample(x)x2x[idxs]Y2Y[idxs,,drop=FALSE]Y2scolBinnedSmoothing(Y2,x=x2,xOut=x2)stopifnot(all(attr(Y2s,"xOut")==x2))stopifnot(all(attr(Y2s,"counts")==1))stopifnot(all(Y2s==Y2))xOutx[seq(from=2,to=J,by=3)]YsTcolBinnedSmoothing(Y,x=x,xOut=xOut)stopifnot(all(YsT==Ys3))stopifnot(all(attr(YsT,"counts")==3))xOutx[seq(from=3,to=J,by=5)]YsTcolBinnedSmoothing(Y,x=x,xOut=xOut)stopifnot(all(YsT==Ys5))stopifnot(all(attr(YsT,"counts")==5)) colKernelSmoothing.matrixKernelsmoothingofamatrixcolumnbycolumn DescriptionKernelsmoothingofamatrixcolumnbycolumn.Usage##S3methodforclass'matrix'colKernelSmoothing(Y,x=seq_len(nrow(Y)),w=NULL,xOut=x,kernel=c("gaussian","uniform"),h,censorH=3,na.rm=TRUE,robust=FALSE,...,verbose=FALSE)ArgumentsYAnumericJxImatrix(oravectoroflengthJ.)xA(optional)numericvectorspecifyingthepositionsoftheJentries.Thedefaultistoassumeuniformlydistributedpositions. 72colKernelSmoothing.matrixwAoptionalnumericvectorofpriorweightsforeachoftheJentries.xOutAnumericvectorspecifyingKtargetpositionswherethekernelisapplied.kernelAcharacterstringorafunctionspecifyingthekernelused.hAsinglepositivenumericspecifyingthebandwidthofthekernel.censorHAsinglepositivenumericspecifyingthewheretotruncatethekernel.IfInf,notruncationisdone.na.rmIfTRUE,missingvaluesareexcluded,otherwisenot.robustIfTRUE,robustestimatorsareused,otherwisenot....Notused.verboseSeeVerbose.ValueReturnsanumericKxImatrix(oravectoroflengthK).Author(s)HenrikBengtssonSeeAlso*colBinnedSmoothing().ExamplesJ100I4Ymatrix(rnorm(I*J,sd=1/2),ncol=I)#Introduceagainincolumn2and3Y[30:50,2:3]Y[30:50,2:3]+3x1:JxOutxYs1colKernelSmoothing(Y,x=x,xOut=xOut,kernel="gaussian",h=1)Ys5colKernelSmoothing(Y,x=x,xOut=xOut,kernel="gaussian",h=5)xlimrange(c(x,xOut))ylimc(-3,5)layout(matrix(1:I,ncol=1))par(mar=c(3,3,1,1)+0.1,pch=19)for(iiin1:I){plot(NA,xlim=xlim,ylim=ylim)points(x,Y[,ii],col="#999999")lines(xOut,Ys1[,ii],col=2)points(xOut,Ys1[,ii],col=2)lines(xOut,Ys5[,ii],col=3)points(xOut,Ys5[,ii],col=3)} CopyNumberChromosomalModel73 CopyNumberChromosomalModelTheCopyNumberChromosomalModelclass DescriptionPackage:aroma.coreClassCopyNumberChromosomalModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModelDirectlyknownsubclasses:CbsModel,CopyNumberSegmentationModel,GladModel,HaarSegModel,RawCopyNumberModelpublicabstractstaticclassCopyNumberChromosomalModelextendsChromosomalModelThisabstractclassrepresentsacopy-numbermodel.UsageCopyNumberChromosomalModel(cesTuple=NULL,refTuple=NULL,calculateRatios=TRUE,tags="*",genome="Human",chromosomes=NULL,maxNAFraction=1/5,...)ArgumentscesTupleACopyNumberDataSetTuple.refTupleAnoptionalCopyNumberDataFile,orCopyNumberDataSetorCopyNumberDataSetTupleforpairwisecomparisons.calculateRatiosAlogicalspecifyingwhetherratiosshouldbecalculatedrelativetotherefer-ence.IfFALSE,argumentrefTupleisignored.tagsAcharactervectoroftags.genomeAcharacterstringspecifyingwhatgenomeisprocess.chromosomes(optional)Avectorspecifyingwhichchromosomestoprocess.maxNAFractionAdoublein[0,1]indicatinghowmanynon-nitesignalsareallowedinthesanitychecksofthedata....Optionalargumentsthatmaybeusedbysomeofthesubclassmodels. 74CopyNumberSegmentationModelFieldsandMethodsMethods:extractRawCopyNumbersExtractsrelativecopynumbers.fitFitsthemodel.getChromosomeLength-getNames-getReference-isPaired-MethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisRequirementsThisclassrequiresgenomeinformationannotationlesforeverychiptype.Author(s)HenrikBengtsson CopyNumberSegmentationModelTheCopyNumberSegmentationModelclass DescriptionPackage:aroma.coreClassCopyNumberSegmentationModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModel~~~~~~~~~~~~| CopyNumberSegmentationModel75~~~~~~~~~~~~+--CopyNumberSegmentationModelDirectlyknownsubclasses:CbsModel,GladModel,HaarSegModelpublicabstractstaticclassCopyNumberSegmentationModelextendsCopyNumberChromosomalModelThisabstractclassrepresentsacopy-numbersegmentationmodel.UsageCopyNumberSegmentationModel(...)Arguments...ArgumentspassedtoconstructorCopyNumberChromosomalModel.FieldsandMethodsMethods:fitFitsthemodel.getFullNames-getRegions-getTags-plot-writeRegions-MethodsinheritedfromCopyNumberChromosomalModel:as.character,calculateChromosomeStatistics,calculateRatios,estimateSds,extractRawCopyNum-bers,t,getChromosomeLength,getDataFileMatrix,getMaxNAFraction,getNames,getOption-alArguments,getPairedNames,getRefSetTuple,getReference,getReferenceSetTuple,isPaired,new-Plot,plotAxesLayers,plotChromosomesLayers,plotCytobandLayers,plotFitLayers,plotGridHor-izontalLayers,plotRawCopyNumbers,plotSampleLayers,setReferenceMethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThis 76doCBSAuthor(s)HenrikBengtsson doCBSPerformsCircularBinarySegmentation(CBS)onadataset DescriptionPerformsCircularBinarySegmentation(CBS)onadatasetforoneormorechiptypes.Usage##DefaultS3method:doCBS(dataSet,tags=NULL,chipTypes,arrays=NULL,...,verbose=FALSE)##S3methodforclass'CopyNumberDataSet'doCBS(ds,arrays=NULL,...)##S3methodforclass'CopyNumberDataSetTuple'doCBS(dsTuple,arrays=NULL,...,verbose=FALSE)Argumentsds,dsTuple,dataSetACopyNumberDataSet,aCopyNumberDataSetTupleoracharacterstringwiththenameofoneofthem.tagsAnoptionalcharactervectorofdatasettags(onlywhendataSetisspeci-ed).chipTypesAcharactervectorspecifyingthechiptypesforthedifferentdatasets(onlywhendataSetisspecied).arraysAnoptionalvectorspecifyingthesubsetofarraystoprocess....AdditionalargumentspassedtoCbsModelanditsfit()method.verboseAlogicalorVerbose.ValueReturnstheoutputdatasetofCbsModel.Author(s)HenrikBengtsson Explorer77Examples##Notrun:dataSet"GSE20939"tags"ACC,-XY,BPN,-XY,RMA,FLN,-XY"chipTypesc("Mapping250K_Nsp","Mapping250K_Sty")fitdoCBS(dataSet,tags=tags,chipTypes=chipTypes,verbose=-10)print(fit)##End(Notrun) ExplorerTheExplorerclass DescriptionPackage:aroma.coreClassExplorerObject~~|~~+--ExplorerDirectlyknownsubclasses:ChromosomeExplorerpublicabstractstaticclassExplorerextendsObjectUsageExplorer(tags="*",version="0",...)ArgumentstagsAcharactervectoroftagstobeaddedtotheoutputpath.versionAnoptionalcharacterstring....Notused. 78GladModelFieldsandMethodsMethods:displayDisplaystheexplorerinthedefaultbrowser.getFullName-getNameGetsthenameoftheexplorer.getNamesGetsthenamesoftheinputsamples.getPathGetsthepathoftheoutputdirectory.getRootPathGetstherootpathoftheoutputdirectory.getTagsGetsthetagsoftheexplorer.getVersion-nbrOfArraysGetsthetotalnumberofarrays.processGeneratesimageles,scriptsanddynamicpagesfortheexplorer.setArraysSetsthearrays.MethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisOutputdirectorystructureThemaindirectoryofanExplorerreportis&#xname;&#xsubn; me0;reports/.The&#xname;istypicallythesameasthenameoftheinputdataset,andthe&#xsubn; me0;istypicallythetagsofditto.ThismaindirectoryiswheremainHTMLdocumentisstored.Foreachchiptype,realor"virtual"(combined),thereisasubdirectorywiththesamenameasthechiptype,i.e.&#xname;&#xsubn; me0;hip;&#xtype;reports/.Foreachchiptypedirectory,therearesetofsubdirectorieseachspecifyingasocalledimagelayer,e.g.animagelayershowingtherawdata,anothercontainingtheestimatesofamodeltandsoon.Pathformat:&#xname;&#xsubn; me0;hip;&#xtype;reports/&#ximag;-25;�layer/.Inthisdirectoryallimagelesarestored,e.g.PNGles.Insomecasesonedonotwanttoallinputtagstobecomepartofthesubname,butinsteadforinstanceusethosetonametheimagelayer(s).Insuchcasesonehastooverridethedefaultnames.Author(s)HenrikBengtsson GladModelTheGladModelclass GladModel79DescriptionPackage:aroma.coreClassGladModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModel~~~~~~~~~~~~|~~~~~~~~~~~~+--CopyNumberSegmentationModel~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--GladModelDirectlyknownsubclasses:publicstaticclassGladModelextendsCopyNumberSegmentationModelThisclassrepresentstheGainandLossAnalysisofDNAregions(GLAD)model[1].Thisclasscanmodelchip-effectestimatesobtainedfrommultiplechiptypes,andnotallsampleshavetobeavailableonallchiptypes.UsageGladModel(cesTuple=NULL,...)ArgumentscesTupleACopyNumberDataSetTuple....ArgumentspassedtotheconstructorofCopyNumberSegmentationModel.DetailsDatafrommultiplechiptypesarecombined"asis".Thisisbasedontheassumptionthattherelativechipeffectestimatesarenon-biased(orattheequallybiasedacrosschiptypes).NotethatinGLADthereisnowaytodownweightcertaindatapoints,whichiswhywecancontrolfordifferencesinvarianceacrosschiptypes.FieldsandMethodsMethods:writeRegions- 80HaarSegModelMethodsinheritedfromCopyNumberSegmentationModel:t,getAsteriskTags,getFitFunction,getFullNames,getRegions,getTags,plot,plotCopyNumber-RegionLayers,writeRegionsMethodsinheritedfromCopyNumberChromosomalModel:as.character,calculateChromosomeStatistics,calculateRatios,estimateSds,extractRawCopyNum-bers,t,getChromosomeLength,getDataFileMatrix,getMaxNAFraction,getNames,getOption-alArguments,getPairedNames,getRefSetTuple,getReference,getReferenceSetTuple,isPaired,new-Plot,plotAxesLayers,plotChromosomesLayers,plotCytobandLayers,plotFitLayers,plotGridHor-izontalLayers,plotRawCopyNumbers,plotSampleLayers,setReferenceMethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisBenchmarkingInhigh-densitycopynumbersanalysis,themosttimeconsumingstepisttingtheGLADmodel.Thecomplexityofthemodelgrowsmorethanlinearly(squared?exponentially?)withthenumberofdatapointsinthechromosomeandsamplebeingtted.Thisiswhyittakemuchmorethantwicethetimetottwochiptypestogetherthanseparately.Author(s)HenrikBengtssonReferences[1]HupePetal.AnalysisofarrayCGHdata:fromsignalratiotogainandlossofDNAregions.Bioinformatics,2004,20,3413-3422.SeeAlsoCopyNumberSegmentationModel. HaarSegModelTheHaarSegModelclass HaarSegModel81DescriptionPackage:aroma.coreClassHaarSegModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModel~~~~~~~~~~~~|~~~~~~~~~~~~+--CopyNumberSegmentationModel~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--HaarSegModelDirectlyknownsubclasses:publicstaticclassHaarSegModelextendsCopyNumberSegmentationModelThisclassrepresentstheHaarwavelet-basedsegmentation(HaarSeg)model[1].UsageHaarSegModel(cesTuple=NULL,...,breaksFdrQ=1e-04)ArgumentscesTupleACopyNumberDataSetTuple.breaksFdrQDefaulttuningparametersspecictotheHaarSegalgorithm....ArgumentspassedtotheconstructorofCopyNumberSegmentationModel.FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromCopyNumberSegmentationModel:t,getAsteriskTags,getFitFunction,getFullNames,getRegions,getTags,plot,plotCopyNumber-RegionLayers,writeRegionsMethodsinheritedfromCopyNumberChromosomalModel:as.character,calculateChromosomeStatistics,calculateRatios,estimateSds,extractRawCopyNum-bers,t,getChromosomeLength,getDataFileMatrix,getMaxNAFraction,getNames,getOption-alArguments,getPairedNames,getRefSetTuple,getReference,getReferenceSetTuple,isPaired,new-Plot,plotAxesLayers,plotChromosomesLayers,plotCytobandLayers,plotFitLayers,plotGridHor-izontalLayers,plotRawCopyNumbers,plotSampleLayers,setReference 82NonPairedPSCNDataMethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtssonReferences[1]Ben-YaacovE.andEldarYC.AfastandexiblemethodforthesegmentationofaCGHdata,Bioinformatics,2008.http://www.ee.technion.ac.il/Sites/People/YoninaEldar/Info/software/HaarSeg.htmSeeAlsoCopyNumberSegmentationModel. NonPairedPSCNDataTheNonPairedPSCNDataclass DescriptionPackage:aroma.coreClassNonPairedPSCNDatadata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--AbstractCNData~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AbstractPSCNData~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--NonPairedPSCNDataDirectlyknownsubclasses: NonPairedPSCNData83publicclassNonPairedPSCNDataextendsAbstractPSCNDataANonPairedPSCNDataobjectholdsparent-speciccopynumberdata.TwoNonPairedPSCNDataobjectsforamatchedtumor-normalpaircanbecombinedintoaPairedPSCNDataobject.UsageNonPairedPSCNData(chromosome=NULL,x=NULL,isSNP=NULL,mu=NULL,C=NULL,beta=NULL,...)ArgumentsCAnumericvectorofJtumortotalcopynumber(TCN)ratiosin[0,+Inf)(duetonoise,smallnegativevaluesarealsoallowed).TheTCNratiosaretypicallyscaledsuchthatcopy-neutraldiploidlocihaveameanoftwo.betaAnumericvectorofJtumoralleleBfractions(BAFs)in[0,1](duetonoise,valuesmaybeslightlyoutsideaswell)orNAfornon-polymorphicloci.muAnoptionalnumericvectorofJgenotypecallsin{0,1/2,1}forAA,AB,andBB,respectively,andNAfornon-polymorphicloci.Ifnotgiven,theyareesti-matedfromthenormalBAFsusingcallNaiveGenotypesasdescribedin[2].isSNPAnoptionallogicalvectoroflengthJspecifyingwhethereachlocusisaSNPornot(non-polymorphicloci).chromosome(Optional)Anintegerscalar(oravectoroflengthJ),whichcanbeusedtospecifywhichchromosomeeachlocusbelongstoincasemultiplechromosomesaresegments.Thisargumentisalsousedforannotationpurposes.xOptionalnumericvectorofJgenomiclocations.IfNULL,indexlocations1:Jareused....Optionalnamedlocus-specicsignalvectorsoflengthJ.FieldsandMethodsMethods:as-as.NonPairedPSCNData-as.PairedPSCNData-callNaiveGenotypes-callSegmentationOutliers-dropSegmentationOutliers-getSignalColumnNames-segmentByCBS-MethodsinheritedfromAbstractPSCNData:callSNPs,getSNPFieldsMethodsinheritedfromAbstractCNData: 84PairedPSCNDatandLargeGaps,getChipType,getLocusData,getPlatform,hasKnownPositions,orderAlongGenome,setChipType,setPlatformMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson PairedPSCNDataThePairedPSCNDataclass DescriptionPackage:aroma.coreClassPairedPSCNDatadata.frame~~|~~+--RichDataFrame PairedPSCNData85~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--AbstractCNData~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--AbstractPSCNData~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--PairedPSCNDataDirectlyknownsubclasses:publicclassPairedPSCNDataextendsAbstractPSCNDataAPairedPSCNDataobjectholdspairedtumor-normalparent-speciccopynumberdata.UsagePairedPSCNData(chromosome=NULL,x=NULL,isSNP=NULL,muN=NULL,CT=NULL,betaT=NULL,CN=NULL,betaN=NULL,...)ArgumentsCTAnumericvectorofJtumortotalcopynumber(TCN)ratiosin[0,+Inf)(duetonoise,smallnegativevaluesarealsoallowed).TheTCNratiosaretypicallyscaledsuchthatcopy-neutraldiploidlocihaveameanoftwo.CNAnoptionalnumericvectorofJnormalTCNratios.betaTAnumericvectorofJtumoralleleBfractions(BAFs)in[0,1](duetonoise,valuesmaybeslightlyoutsideaswell)orNAfornon-polymorphicloci.betaNAnumericvectorofJmatchednormalBAFsin[0,1](duetonoise,valuesmaybeslightlyoutsideaswell)orNAfornon-polymorphicloci.muNAnoptionalnumericvectorofJgenotypecallsin{0,1/2,1}forAA,AB,andBB,respectively,andNAfornon-polymorphicloci.Ifnotgiven,theyareesti-matedfromthenormalBAFsusingcallNaiveGenotypesasdescribedin[2].isSNPAnoptionallogicalvectoroflengthJspecifyingwhethereachlocusisaSNPornot(non-polymorphicloci).chromosome(Optional)Anintegerscalar(oravectoroflengthJ),whichcanbeusedtospecifywhichchromosomeeachlocusbelongstoincasemultiplechromosomesaresegments.Thisargumentisalsousedforannotationpurposes.xOptionalnumericvectorofJgenomiclocations.IfNULL,indexlocations1:Jareused....Optionalnamedlocus-specicsignalvectorsoflengthJ. 86PairedPSCNDataFieldsandMethodsMethods:as-as.PairedPSCNData-callNaiveGenotypes-callSegmentationOutliers-dropSegmentationOutliers-getSignalColumnNames-getTCNs-getTotalCopyNumbers-normalizeTumorBoost-plotTracks-segmentByCBS-segmentByPairedPSCBS-MethodsinheritedfromAbstractPSCNData:callSNPs,getSNPFieldsMethodsinheritedfromAbstractCNData:ndLargeGaps,getChipType,getLocusData,getPlatform,hasKnownPositions,orderAlongGenome,setChipType,setPlatformMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass- ParametersInterface87method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson ParametersInterfaceTheParametersInterfaceclassinterface DescriptionPackage:aroma.coreClassParametersInterfaceInterface~~|~~+--ParametersInterfaceDirectlyknownsubclasses:AromaTransformpublicclassParametersInterfaceextendsInterfaceUsageParametersInterface(...)Arguments...Notused.FieldsandMethodsMethods:getParameters-getParametersAsString-MethodsinheritedfromInterface: 88RawAlleleBFractionsextend,print,usesAuthor(s)HenrikBengtsson RawAlleleBFractionsTheRawAlleleBFractionsclass DescriptionPackage:aroma.coreClassRawAlleleBFractionsdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawAlleleBFractionsDirectlyknownsubclasses:RawMirroredAlleleBFractions,SegmentedAlleleBFractionspublicclassRawAlleleBFractionsextendsRawGenomicSignalsUsageRawAlleleBFractions(...)Arguments...ArgumentspassedtoRawGenomicSignals.FieldsandMethodsMethods:extractRawMirroredAlleleBFractions-plot- RawCopyNumberModel89MethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson RawCopyNumberModelTheRawCopyNumberModelclass DescriptionPackage:aroma.coreClassRawCopyNumberModelObject~~|~~+--ChromosomalModel~~~~~~~|~~~~~~~+--CopyNumberChromosomalModel 90RawCopyNumberModel~~~~~~~~~~~~|~~~~~~~~~~~~+--RawCopyNumberModelDirectlyknownsubclasses:publicabstractstaticclassRawCopyNumberModelextendsCopyNumberChromosomalModelThisclassrepresentsanidentitycopy-numbermodelwhichreturnstheinputasis.UsageRawCopyNumberModel(...)Arguments...Passedtotheconstructorofthesuperclass.FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromCopyNumberChromosomalModel:as.character,calculateChromosomeStatistics,calculateRatios,estimateSds,extractRawCopyNum-bers,t,getChromosomeLength,getDataFileMatrix,getMaxNAFraction,getNames,getOption-alArguments,getPairedNames,getRefSetTuple,getReference,getReferenceSetTuple,isPaired,new-Plot,plotAxesLayers,plotChromosomesLayers,plotCytobandLayers,plotFitLayers,plotGridHor-izontalLayers,plotRawCopyNumbers,plotSampleLayers,setReferenceMethodsinheritedfromChromosomalModel:as.character,t,getAlias,getAromaGenomeTextFile,getAsteriskTags,getChipType,getChipTypes,getChromosomes,getFullName,getFullNames,getGenome,getGenomeData,getGenomeFile,getListO-fAromaUgpFiles,getName,getNames,getParentPath,getPath,getReportPath,getRootPath,get-SetTuple,getSets,getTags,indexOf,nbrOfArrays,nbrOfChipTypes,setChromosomes,setGenomeMethodsinheritedfromObject:$,$[[,[[as.character,attach,attachLocally,clearCache,clearLookupCache,clone,detach,equals,extend,nalize,getEnvironment,getFieldModier,getFieldModiers,getFields,getInstan-tiationTime,getStaticInstance,hasField,hashCode,ll,load,names,objectSize,print,save,asThisAuthor(s)HenrikBengtsson RawCopyNumbers91 RawCopyNumbersTheRawCopyNumbersclass DescriptionPackage:aroma.coreClassRawCopyNumbersdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawCopyNumbersDirectlyknownsubclasses:SegmentedCopyNumberspublicclassRawCopyNumbersextendsRawGenomicSignalsUsageRawCopyNumbers(cn=NULL,...)ArgumentscnAnumericvectoroflengthJspecifyingthecopynumberateachloci....ArgumentspassedtoRawGenomicSignals.FieldsandMethodsMethods:cnRange-extractRawCopyNumbers-getSignals-plot-MethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat- 92RawCopyNumberseStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtssonExamples#-----------------------------#Simulatingcopy-numberdata#-----------------------------#NumberoflociJ1000mudouble(J)mu[200:300]mu[200:300]+1mu[650:800]mu[650:800]-1epsrnorm(J,sd=1/2)ymu+epsxsort(runif(length(y),max=length(y)))cnRawCopyNumbers(y,x)print(cn)cn2extractSubset(cn,subset=xSeq(cn,by=5)) RawCopyNumbers93print(cn2)#-----------------------------#Plotalonggenome#-----------------------------plot(cn,ylim=c(-3,3))title(main="Completeandsubsettedloci")points(cn2,col="red",pch=176,cex=2)legend("topright",pch=c(19,176),col=c("#999999","red"),sprintf(c("raw[n=%d]","every5th[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cn2))),bty="n")#-----------------------------#Binnedsmoothing#-----------------------------plot(cn,col="#999999",ylim=c(-3,3))title(main="Binnedsmoothing")cnSabinnedSmoothing(cn,by=3)lines(cnSa,col="blue")points(cnSa,col="blue")cnSbbinnedSmoothing(cn,by=9)lines(cnSb,col="red")points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","Bin(w=3)[n=%d]","Bin(w=9)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n")#-----------------------------#Binnedsmoothing(bycount)#-----------------------------plot(cn,col="#999999",ylim=c(-3,3))title(main="Binnedsmoothing(bycount)")cnSabinnedSmoothing(cn,by=3,byCount=TRUE)lines(cnSa,col="blue")points(cnSa,col="blue")cnSbbinnedSmoothing(cn,by=9,byCount=TRUE)lines(cnSb,col="red")points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","BinO(w=3)[n=%d]","BinO(w=9)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n")#----------------------------- 94RawGenomicSignals#Kernelsmoothing(defaultisGaussian)#-----------------------------plot(cn,col="#999999",ylim=c(-3,3))title(main="Kernelsmoothingw/Gaussiankernel")cnSakernelSmoothing(cn,h=2)points(cnSa,col="blue")cnSbkernelSmoothing(cn,h=5)points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","N(.,sd=2)[n=%d]","N(.,sd=5)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n")#-----------------------------#Kernelsmoothing#-----------------------------plot(cn,col="#999999",ylim=c(-3,3))title(main="Kernelsmoothingw/uniformkernel")xOutxSeq(cn,by=10)cnSakernelSmoothing(cn,xOut=xOut,kernel="uniform",h=2)lines(cnSa,col="blue")points(cnSa,col="blue")cnSbkernelSmoothing(cn,xOut=xOut,kernel="uniform",h=5)lines(cnSb,col="red")points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","U(w=2)[n=%d]","U(w=5)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n") RawGenomicSignalsTheRawGenomicSignalsclass DescriptionPackage:aroma.coreClassRawGenomicSignalsdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals RawGenomicSignals95Directlyknownsubclasses:AbstractCNData,AbstractPSCNData,NonPairedPSCNData,PairedPSCNData,RawAlleleBFrac-tions,RawCopyNumbers,RawMirroredAlleleBFractions,RawSequenceReads,SegmentedAlleleBFrac-tions,SegmentedCopyNumberspublicclassRawGenomicSignalsextendsRichDataFrameUsageRawGenomicSignals(y=NULL,x=NULL,w=NULL,chromosome=0L,name=NULL,...)ArgumentsyAnumericvectoroflengthJspecifyingthesignalateachlocus.xA(optional)numericvectoroflengthJspecifyingthepositionofeachlocus.wA(optional)non-negativenumericvectoroflengthJspecifyingaweightofeachlocus.chromosomeAn(optional)integerspecifyingthechromosomeforthesegenomicsignals.nameAn(optional)characterstringspecifyingthesamplename....Notused.FieldsandMethodsMethods:*-+---addBy-append-as.data.frame-binnedSmoothing-divideBy-drawDensity-estimateStandardDeviation-gaussianSmoothing-getChromosome-getChromosomes-getPositions-getSigma-getSignals-getWeights-getXScale-getYScale-hasWeights- 96RawGenomicSignalskernelSmoothing-lines-multiplyBy-nbrOfChromosomes-nbrOfLoci-plot-points-segmentByCBS-segmentByGLAD-segmentByHaarSeg-segmentByMPCBS-setSigma-setSignals-setWeights-setXScale-setYScale-signalRange-sort-subtractBy-xMax-xMin-xRange-xSeq-yMax-yMin-yRange-MethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,attachLocally,by,callSegmentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSeg-mentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,formula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,transform,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrame RawMirroredAlleleBFractions97Author(s)HenrikBengtsson RawMirroredAlleleBFractionsTheRawMirroredAlleleBFractionsclass DescriptionPackage:aroma.coreClassRawMirroredAlleleBFractionsdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawAlleleBFractions~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--RawMirroredAlleleBFractionsDirectlyknownsubclasses:publicclassRawMirroredAlleleBFractionsextendsRawAlleleBFractionsUsageRawMirroredAlleleBFractions(...)Arguments...ArgumentspassedtoRawAlleleBFractions.FieldsandMethodsMethods:plot-MethodsinheritedfromRawAlleleBFractions: 98RawSequenceReadsextractRawMirroredAlleleBFractions,plotMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,as.proleCGH,attachLocally,by,callSeg-mentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSegmentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,for-mula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,trans-form,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson RawSequenceReadsTheRawSequenceReadsclass DescriptionPackage:aroma.coreClassRawSequenceReadsdata.frame~~|~~+--RichDataFrame~~~~~~~| RawSequenceReads99~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawSequenceReadsDirectlyknownsubclasses:publicclassRawSequenceReadsextendsRawGenomicSignalsUsageRawSequenceReads(x=NULL,y=rep(1L,length(x)),...)ArgumentsxAnintegervectoroflengthJspecifyingthereadpositions.yAn(optional)integervectoroflengthJspecifyingthenumberofreadsateachposition.Defaultisonereadperposition....ArgumentspassedtoRawGenomicSignals.FieldsandMethodsMethods:binnedSums-extractRawCopyNumbers-nbrOfReads-plot-MethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction, 100SegmentedAlleleBFractionsgetVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,as.proleCGH,attachLocally,by,callSeg-mentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSegmentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,for-mula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,trans-form,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtsson SegmentedAlleleBFractionsTheSegmentedAlleleBFractionsclass DescriptionPackage:aroma.coreClassSegmentedAlleleBFractionsdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawAlleleBFractions~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--SegmentedGenomicSignalsInterface~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--SegmentedAlleleBFractionsDirectlyknownsubclasses:publicclassSegmentedAlleleBFractionsextendsSegmentedGenomicSignalsInterface SegmentedAlleleBFractions101UsageSegmentedAlleleBFractions(...,states=NULL)Arguments...ArgumentspassedtoRawAlleleBFractions.statesAfunctionreturningthecopy-numberstatesgivenavectoroflocuspositions.FieldsandMethodsMethods:Nomethodsdened.MethodsinheritedfromSegmentedGenomicSignalsInterface:as.data.frame,binnedSmoothingByState,extractSubsetByState,ndChangePointsByState,getState-ColorMap,getStateColors,getStates,getUniqueStates,getVirtualField,getVirtualLocusFields,ker-nelSmoothingByState,plot,points,setStateColorMap,setStatesMethodsinheritedfromRawAlleleBFractions:extractRawMirroredAlleleBFractions,plotMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,as.proleCGH,attachLocally,by,callSeg-mentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSegmentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,for-mula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,trans-form,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrame 102SegmentedCopyNumbersAuthor(s)HenrikBengtsson SegmentedCopyNumbersTheSegmentedCopyNumbersclass DescriptionPackage:aroma.coreClassSegmentedCopyNumbersdata.frame~~|~~+--RichDataFrame~~~~~~~|~~~~~~~+--RawGenomicSignals~~~~~~~~~~~~|~~~~~~~~~~~~+--RawCopyNumbers~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~+--SegmentedGenomicSignalsInterface~~~~~~~~~~~~~~~~~~~~~~|~~~~~~~~~~~~~~~~~~~~~~+--SegmentedCopyNumbersDirectlyknownsubclasses:publicclassSegmentedCopyNumbersextendsSegmentedGenomicSignalsInterfaceUsageSegmentedCopyNumbers(...,states=NULL)Arguments...ArgumentspassedtoRawCopyNumbers.statesAfunctionreturningthecopy-numberstatesgivenavectoroflocuspositions.FieldsandMethodsMethods:Nomethodsdened. SegmentedCopyNumbers103MethodsinheritedfromSegmentedGenomicSignalsInterface:as.data.frame,binnedSmoothingByState,extractSubsetByState,ndChangePointsByState,getState-ColorMap,getStateColors,getStates,getUniqueStates,getVirtualField,getVirtualLocusFields,ker-nelSmoothingByState,plot,points,setStateColorMap,setStatesMethodsinheritedfromRawCopyNumbers:cnRange,extractRawCopyNumbers,getCNs,getCn,getSignals,plotMethodsinheritedfromRawGenomicSignals:*,+,-,addBy,append,applyBinaryOperator,as.character,as.data.frame,assertOneChromosome,binnedSmoothing,binnedSmoothingByField,clearCache,clone,divideBy,drawDensity,estimat-eStandardDeviation,extractChromosome,extractChromosomes,extractDataForSegmentation,ex-tractRegion,extractRegions,extractSubset,gaussianSmoothing,getBasicField,getCXY,getChro-mosome,getChromosomes,getDefaultLocusFields,getLocusFields,getPositions,getSigma,getSig-nalColumnName,getSignalColumnNames,getSignals,getWeights,getXScale,getXY,getYScale,hasWeights,kernelSmoothing,lines,multiplyBy,nbrOfChromosomes,nbrOfLoci,plot,points,print,segmentByCBS,segmentByGLAD,segmentByHaarSeg,segmentByMPCBS,setBasicField,setSigma,setSignals,setWeights,setXScale,setYScale,signalRange,sort,subtractBy,xMax,xMin,xRange,xSeq,yMax,yMin,yRangeMethodsinheritedfromRichDataFrame:$,$[,[[,[[as.data.frame,as.list,dim,dropVirtualColumn,getColumnNames,getColumn-NamesTranslator,getFullName,getName,getTags,getVirtualColumn,getVirtualColumnFunction,getVirtualColumnNames,hasColumn,hasColumns,hasVirtualColumn,hasVirtualColumns,length,names,newInstance,print,rbind,setAttributes,setColumnNamesMap,setColumnNamesTransla-tor,setName,setTags,setVirtualColumn,subset,translateColumnNamesMethodsinheritedfromdata.frame:$$Math,Ops,nonStructure,vector-method,Ops,structure,vector-method,Ops,vector,nonStructure-method,Ops,vector,structure-method,Ops,Summary,[,[method,[[[,[[[[aggregate,anyDuplicated,as.NonPairedPSCNData,as.PairedPSCNData,as.data.frame,as.list,as.matrix,as.proleCGH,attachLocally,by,callSeg-mentationOutliers,cbind,coerce,ANY,list-method,coerce,oldClass,S3-method,dim,dimnames,dimnamesdropSegmentationOutliers,droplevels,duplicated,edit,ndLargeGaps,format,for-mula,head,initialize,oldClass-method,is.na,merge,na.exclude,na.omit,plot,plotDensity,print,prompt,rbind,row.names,row.namesrowsum,segmentByCBS,segmentByPairedPSCBS,show,oldClass-method,slotsFromS3,data.frame-method,split,splitstack,str,subset,summary,t,tail,trans-form,type.convert,unique,unstack,unwrap,within,wrap,writeDataFrameAuthor(s)HenrikBengtssonExamples#-----------------------------#Simulatingcopy-numberdata#-----------------------------#TrueCNstatesstateFcnfunction(x,...){statesinteger(length(x))states[200&x300]-1L 104SegmentedCopyNumbersstates[650&x800]+1Lstates}#NumberoflociJ1000yrnorm(J,sd=1/2)x1:length(y)for(stateinc(-1,+1)){idxs(stateFcn(x)==state)y[idxs]y[idxs]+state}cnSegmentedCopyNumbers(y,x,states=stateFcn)print(cn)#-----------------------------#Subsetting#-----------------------------plot(cn,ylim=c(-4,4))title("Copynumbersannotatedbystate(andsubsetbystate)")cnSextractSubsetByState(cn,states=c(0,+1L))print(cnS)points(cnS,pch=21,cex=1.2,lwd=2,col="purple")legend("topright",pch=c(19,21),col=c("#999999","purple"),sprintf(c("raw[n=%d]","CNin{0,1}[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnS))),bty="n")#-----------------------------#Kernelsmoothingstratifiedbystate#-----------------------------plot(cn,col="#999999",ylim=c(-3,3))title(main="Kernelsmoothingstratifiedbystatew/Gaussiankernel")cnSakernelSmoothingByState(cn,h=2)points(cnSa,col="blue")cnSbkernelSmoothingByState(cn,h=5)points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","N(.,sd=2)[n=%d]","N(.,sd=5)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n")#-----------------------------#Binnedsmoothingstratifiedbystate#----------------------------- SegmentedGenomicSignalsInterface105plot(cn,col="#999999",ylim=c(-3,3))title(main="Binnedsmoothingstratifiedbystate")cnSabinnedSmoothingByState(cn,by=3,verbose=-1)lines(cnSa,col="blue")points(cnSa,col="blue")cnSbbinnedSmoothingByState(cn,by=9,verbose=-1)lines(cnSb,col="red")points(cnSb,col="red")legend("topright",pch=19,col=c("#999999","blue","red"),sprintf(c("raw[n=%d]","Bin(w=3)[n=%d]","Bin(w=9)[n=%d]"),c(nbrOfLoci(cn),nbrOfLoci(cnSa),nbrOfLoci(cnSb))),bty="n") SegmentedGenomicSignalsInterfaceTheSegmentedGenomicSignalsInterfaceclassinterface DescriptionPackage:aroma.coreClassSegmentedGenomicSignalsInterfaceInterface~~|~~+--SegmentedGenomicSignalsInterfaceDirectlyknownsubclasses:SegmentedAlleleBFractions,SegmentedCopyNumberspublicclassSegmentedGenomicSignalsInterfaceextendsInterfaceUsageSegmentedGenomicSignalsInterface(...)Arguments...Notused.FieldsandMethodsMethods: 106UnitAnnotationDataFileas.data.frame-binnedSmoothingByState-extractSubsetByState-findChangePointsByState-getStateColorMap-getStateColors-getStates-getUniqueStates-kernelSmoothingByState-plot-points-setStateColorMap-setStates-MethodsinheritedfromInterface:extend,print,usesAuthor(s)HenrikBengtsson UnitAnnotationDataFileTheUnitAnnotationDataFileinterfaceclass DescriptionPackage:aroma.coreClassUnitAnnotationDataFileInterface~~|~~+--UnitAnnotationDataFileDirectlyknownsubclasses:AromaUFile,AromaUgcFile,AromaUgpFile,AromaUnitChromosomeTabularBinaryFile,Aro-maUnitGcContentFile,AromaUnitTabularBinaryFile,AromaUnitTypesFile,TextUnitNamesFile,UnitNamesFile,UnitTypesFilepublicstaticclassUnitAnnotationDataFileextendsInterfaceAUnitAnnotationDataFileprovidesmethodsforqueryingcertaintypesofchiptypeannotationdatabyunits. UnitNamesFile107UsageUnitAnnotationDataFile(...)Arguments...ArgumentspassedtoInterface.MethodsMethods:byChipType-getAromaUflFile-getAromaUgpFile-getChipType-getPlatform-nbrOfUnits-MethodsinheritedfromInterface:extend,print,usesAuthor(s)HenrikBengtsson UnitNamesFileTheUnitNamesFileinterfaceclass DescriptionPackage:aroma.coreClassUnitNamesFileInterface~~|~~+--UnitAnnotationDataFile~~~~~~~|~~~~~~~+--UnitNamesFileDirectlyknownsubclasses:TextUnitNamesFile 108UnitTypesFilepublicabstractstaticclassUnitNamesFileextendsUnitAnnotationDataFileAUnitNamesFileprovidesmethodsforqueryingtheunitnamesofagivenchiptype.UsageUnitNamesFile(...)Arguments...ArgumentspassedtoUnitAnnotationDataFile.MethodsMethods:getUnitNames-indexOf-nbrOfUnits-MethodsinheritedfromUnitAnnotationDataFile:byChipType,getAromaUFile,getAromaUgpFile,getChipType,getDefaultExtension,getPlatform,nbrOfUnitsMethodsinheritedfromInterface:extend,print,usesAuthor(s)HenrikBengtsson UnitTypesFileTheUnitTypesFileinterfaceclass DescriptionPackage:aroma.coreClassUnitTypesFileInterface~~|~~+--UnitAnnotationDataFile~~~~~~~|~~~~~~~+--UnitTypesFile UnitTypesFile109Directlyknownsubclasses:AromaUnitTypesFilepublicabstractstaticclassUnitTypesFileextendsUnitAnnotationDataFileAUnitTypesFileprovidesmethodsforqueryingtheunittypesofagivenchiptype,e.g.genotypingorcopy-numberunit,exonunitetc.UsageUnitTypesFile(...)Arguments...ArgumentspassedtoUnitAnnotationDataFile.MethodsMethods:getUnitTypes-nbrOfUnits-MethodsinheritedfromUnitAnnotationDataFile:byChipType,getAromaUFile,getAromaUgpFile,getChipType,getDefaultExtension,getPlatform,nbrOfUnitsMethodsinheritedfromInterface:extend,print,usesThearomaunit-typemapunknown=0,expression=1,genotyping=2,resequencing=3,tag=4,copynumber=5,genotypingcon-trol=6,expressioncontrol=7Author(s)HenrikBengtsson IndexTopicarraycolBinnedSmoothing.matrix,68colKernelSmoothing.matrix,71TopicclassesAbstractCNData,4AbstractPSCNData,6AromaCellCpgFile,7AromaCellPositionFile,8AromaCellTabularBinaryFile,9AromaGenomeTextFile,11AromaMicroarrayDataFile,14AromaMicroarrayDataSet,15AromaMicroarrayDataSetTuple,17AromaMicroarrayTabularBinaryFile,18AromaPlatform,21AromaPlatformInterface,22AromaRepository,23AromaTabularBinaryFile,25AromaTabularBinarySet,27AromaTransform,29AromaUnitCallFile,30AromaUnitCallSet,32AromaUnitFracBCnBinaryFile,34AromaUnitFracBCnBinarySet,37AromaUnitGenotypeCallFile,39AromaUnitGenotypeCallSet,41AromaUnitPscnBinaryFile,43AromaUnitPscnBinarySet,46AromaUnitSignalBinaryFile,48AromaUnitSignalBinarySet,50AromaUnitTabularBinaryFile,52AromaUnitTotalCnBinaryFile,54AromaUnitTotalCnBinarySet,57AromaUnitTypesFile,59BinnedScatter,61CbsModel,63ChromosomalModel,65ChromosomeExplorer,66CopyNumberChromosomalModel,73CopyNumberSegmentationModel,74Explorer,77GladModel,78HaarSegModel,80NonPairedPSCNData,82PairedPSCNData,84ParametersInterface,87RawAlleleBFractions,88RawCopyNumberModel,89RawCopyNumbers,91RawGenomicSignals,94RawMirroredAlleleBFractions,97RawSequenceReads,98SegmentedAlleleBFractions,100SegmentedCopyNumbers,102SegmentedGenomicSignalsInterface,105UnitAnnotationDataFile,106UnitNamesFile,107UnitTypesFile,108TopiciterationcolBinnedSmoothing.matrix,68colKernelSmoothing.matrix,71TopicmethodscolBinnedSmoothing.matrix,68colKernelSmoothing.matrix,71Topicpackagearoma.core-package,3TopicrobustcolBinnedSmoothing.matrix,68colKernelSmoothing.matrix,71TopicunivarcolBinnedSmoothing.matrix,68colKernelSmoothing.matrix,71*colBinnedSmoothing,72*colKernelSmoothing,69AbstractCNData,4,6,82,85,95AbstractPSCNData,4,6,82,83,85,95110 INDEX111aroma.core(aroma.core-package),3aroma.core-package,3AromaCellCpgFile,7,9,19,22,25AromaCellPositionFile,8,9,19,22,25AromaCellSequenceFile,9,19,22,25AromaCellTabularBinaryFile,8,9,19,22,25AromaGenomeTextFile,11AromaMicroarrayDataFile,14,16AromaMicroarrayDataSet,15,15,29AromaMicroarrayDataSetTuple,17,65AromaMicroarrayTabularBinaryFile,9,18,22,25,52AromaPlatform,21AromaPlatformInterface,9,19,22,30,35,39,44,48,52,55,59AromaRepository,23AromaTabularBinaryFile,9,10,19,21,25,27,28,30,35,39,44,48,50,52,53,55,59AromaTabularBinarySet,27,33,37,41,46,50,51,57AromaTransform,29,87AromaUcscGenomeTextFile,12AromaUflFile,19,22,25,52,106AromaUgcFile,19,22,25,52,106AromaUgpFile,19,22,25,52,106AromaUnitCallFile,22,25,30,33,39,48AromaUnitCallSet,27,32,42,50AromaUnitChromosomeTabularBinaryFile,19,22,25,52,106AromaUnitFracBCnBinaryFile,22,25,34,37,48AromaUnitFracBCnBinarySet,27,37,50AromaUnitGcContentFile,19,22,25,52,106AromaUnitGenotypeCallFile,22,25,31,39,42,48AromaUnitGenotypeCallSet,27,33,41,50AromaUnitPscnBinaryFile,22,25,43,46,48AromaUnitPscnBinarySet,27,46,50AromaUnitSignalBinaryFile,22,25,31,35,39,44,48,51,55,59AromaUnitSignalBinarySet,27,33,37,42,46,50,57,58AromaUnitTabularBinaryFile,11,19,22,25,35,39,40,52,60,106AromaUnitTotalCnBinaryFile,22,25,48,54,57AromaUnitTotalCnBinarySet,27,50,57AromaUnitTotalCnBinarySetTuple,17AromaUnitTypesFile,22,25,48,59,106,109BinnedScatter,61binnedSmoothing(colBinnedSmoothing.matrix),68CacheKeyInterface,9,11,14,19,25,30,35,39,43,48,52,55,59callNaiveGenotypes,83,85CbsModel,63,65,73,75,76character,4,29,65,72,73,76,77,95ChromosomalModel,63,65,73,74,79,81,89ChromosomeExplorer,66,77colBinnedSmoothing(colBinnedSmoothing.matrix),68colBinnedSmoothing.matrix,68colKernelSmoothing(colKernelSmoothing.matrix),71colKernelSmoothing.matrix,71ColumnNamesInterface,9,11,19,25,30,34,39,43,48,52,55,59CopyNumberChromosomalModel,63,65,67,68,73,74,75,79,81,89,90CopyNumberDataFile,44,55,73CopyNumberDataSet,46,57,73,76CopyNumberDataSetTuple,64,73,76,79,81CopyNumberSegmentationModel,63–65,73,74,79–82display,78doCBS,76double,73downloadChipTypeFile,24Explorer,67,77extractRawCopyNumbers,74FALSE,73FileCacheKeyInterface,9,11,12,14,19,25,30,35,39,43,48,52,55,59fit,74,75FullNameInterface,9,11,14,15,17,19,25,27,30,33,34,37,39,41,43,46,48,50,52,54,57,59function,4,69,72,101,102 112INDEXGenericDataFile,9,11,14,19,25,27,30,34,39,43,48,52,54,59GenericDataFileSet,16,27,28,33,37,41,46,50,57GenericDataFileSetList,17,18GenericTabularFile,9,11,19,25,30,35,39,43,48,52,55,59GenericTabularFileSet,27,33,37,41,46,50,57getAromaPlatform,23getChipType,23,66getChromosomes,66,67getFullName,29getInputDataSet,29getModel,67getName,30,78getNames,66,78getOutputDataSet,30getPath,30,78getPlatform,23getRootPath,30,78getTags,30,78GladModel,65,73,75,78HaarSegModel,65,73,75,80Inf,72,83,85integer,4,6,64,67,83,85,95,99Interface,22,23,87,105–108isDone,30kernelSmoothing(colKernelSmoothing.matrix),71list,4,16,28,62logical,6,73,76,83,85matrix,62,68,69,71,72NA,6,69,83,85nbrOfArrays,66,78nbrOfChipTypes,18,66NonPairedPSCNData,4,6,82,95NULL,4,6,83,85numeric,4,6,62,68,69,71,72,83,85,91,95Object,9,11,14,15,17,19,21,23–25,27,29,30,33,34,37,39,41,43,46,48,50,52,54,57,59,63,65,66,73,74,77,79,81,89PairedPSCNData,4,6,83,84,95ParametersInterface,29,87png2,68process,30,67,78RawAlleleBFractions,88,95,97,100,101RawCopyNumberModel,65,73,89RawCopyNumbers,91,95,102RawGenomicSignals,4,6,82,85,88,91,94,97,99,100,102RawMirroredAlleleBFractions,88,95,97RawSequenceReads,95,98readFooter,26RichDataFrame,4,6,82,84,88,91,94,95,97,98,100,102segmentByCBS,64SegmentedAlleleBFractions,88,95,100,105SegmentedCopyNumbers,91,95,102,105SegmentedGenomicSignalsInterface,100,102,105seq,69setArrays,67,78TabularTextFile,11,12TextUnitNamesFile,106,107TRUE,69,72UnitAnnotationDataFile,52,53,59,106,107–109UnitNamesFile,106,107UnitTypesFile,59,60,106,108vector,4,6,29,65,67–69,71–73,76,77,83,85,91,95,99,101,102Verbose,24,69,72,76writeDataFrame,49,51,53writeFooter,26