Package: aroma.core 3.3.0
aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Authors:
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aroma.core/json (API)
NEWS
| # Install 'aroma.core' in R: |
| install.packages('aroma.core', repos = c('https://henrikbengtsson.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/henrikbengtsson/aroma.core/issues
Last updated 2 years agofrom:1bf20e2b09 (on master). Checks:OK: 2 NOTE: 4 ERROR: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 13 2024 |
| R-4.5-win | NOTE | Aug 13 2024 |
| R-4.5-linux | NOTE | Aug 13 2024 |
| R-4.4-win | NOTE | Aug 13 2024 |
| R-4.4-mac | NOTE | Aug 13 2024 |
| R-4.3-win | ERROR | Aug 13 2024 |
| R-4.3-mac | OK | Aug 13 2024 |
Exports:-.CopyNumberRegions-.RawGenomicSignals.Machine[.AromaTabularBinaryFile[.RasterImage[.RichDataFrame[[.AromaTabularBinaryFile[[.RichDataFrame[[<-.RichDataFrame[<-.AromaTabularBinaryFile*.CopyNumberRegions*.RawGenomicSignals+.CopyNumberRegions+.RawGenomicSignals$.RichDataFrame$<-.RichDataFrameAbstractCNDataAbstractPSCNDataaddByaddBy.RawGenomicSignalsaddIncludesaddIncludes.ExploreraddIndexFileaddIndexFile.ChromosomeExploreraddIndexFile.Explorerallocateallocate.AromaCellCpgFileallocate.AromaCellPositionFileallocate.AromaCellSequenceFileallocate.AromaMicroarrayTabularBinaryFileallocate.AromaTabularBinaryFileallocate.AromaUflFileallocate.AromaUgpFileallocate.AromaUnitCallFileallocate.AromaUnitChromosomeTabularBinaryFileallocate.AromaUnitGenotypeCallFileallocate.AromaUnitPscnBinaryFileallocate.AromaUnitSignalBinaryFileallocate.AromaUnitTypesFileallocateFromUnitAnnotationDataFileallocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFileallocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFileallocateFromUnitNamesFileallocateFromUnitNamesFile.AromaUnitSignalBinaryFileallocateFromUnitNamesFile.AromaUnitTabularBinaryFileappend.CopyNumberRegionsappend.RawGenomicSignalsapplyBinaryOperatorapplyBinaryOperator.RawGenomicSignalsapplyRegionsapplyRegions.CopyNumberOutliersapplyRowsapplyRows.CopyNumberRegionsapplyToapplyTo.SampleAnnotationFilearoma.coreAromaCellCpgFileAromaCellPositionFileAromaCellSequenceFileAromaCellTabularBinaryFileAromaCoreAromaGenomeTextFileAromaMicroarrayDataFileAromaMicroarrayDataSetAromaMicroarrayDataSetTupleAromaMicroarrayTabularBinaryFileAromaPackageAromaPlatformAromaPlatformInterfaceAromaRepositoryaromaSettingsAromaSettingsAromaTabularBinaryFileAromaTabularBinarySetAromaTransformAromaUcscGenomeTextFileAromaUflFileAromaUgcFileAromaUgpFileAromaUnitCallFileAromaUnitCallSetAromaUnitChromosomeTabularBinaryFileAromaUnitFracBCnBinaryFileAromaUnitFracBCnBinarySetAromaUnitGcContentFileAromaUnitGenotypeCallFileAromaUnitGenotypeCallSetAromaUnitPscnBinaryFileAromaUnitPscnBinarySetAromaUnitSignalBinaryFileAromaUnitSignalBinarySetAromaUnitTabularBinaryFileAromaUnitTotalCnBinaryFileAromaUnitTotalCnBinaryFileListAromaUnitTotalCnBinarySetAromaUnitTotalCnBinarySetTupleAromaUnitTypesFileas.AromaMicroarrayDataSetListas.AromaMicroarrayDataSetList.AromaMicroarrayDataSetas.AromaMicroarrayDataSetTupleas.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetas.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetTupleas.AromaUnitTotalCnBinarySetTupleas.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetas.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetTupleas.character.AromaMicroarrayDataSetTupleas.character.AromaMicroarrayTabularBinaryFileas.character.AromaPlatformas.character.AromaTabularBinaryFileas.character.AromaTransformas.character.AromaUnitSignalBinaryFileas.character.ChromosomalModelas.character.ChromosomeExploreras.character.CopyNumberChromosomalModelas.character.CopyNumberOutliersas.character.CopyNumberRegionsas.character.Exploreras.character.RasterImageas.character.RawGenomicSignalsas.character.SegmentationDataSetas.character.TextUnitNamesFileas.CopyNumberDataFileas.CopyNumberDataFile.CopyNumberDataFileas.CopyNumberDataSetas.CopyNumberDataSet.CopyNumberDataSetas.CopyNumberDataSetTupleas.CopyNumberDataSetTuple.AromaUnitTotalCnBinarySetas.CopyNumberDataSetTuple.CopyNumberDataSetTupleas.CopyNumberDataSetTuple.listas.data.frame.CopyNumberOutliersas.data.frame.CopyNumberRegionsas.data.frame.RawGenomicSignalsas.data.frame.RichDataFrameas.data.frame.SegmentedGenomicSignalsInterfaceas.GrayscaleImageas.GrayscaleImage.matrixas.list.RichDataFrameas.NonPairedPSCNDataas.NonPairedPSCNData.data.frameas.NonPairedPSCNData.NonPairedPSCNDataas.PairedPSCNDataas.PairedPSCNData.data.frameas.PairedPSCNData.NonPairedPSCNDataas.PairedPSCNData.PairedPSCNDataassertOneChromosomeassertOneChromosome.RawGenomicSignalsasThisasThis.BasicObjectasThis.ObjectbacktransformGenotypeConebacktransformGenotypeCone.matrixbacktransformMultiDimensionalConebacktransformMultiDimensionalCone.matrixbarSequencebarSequence.ProbePositionEffectsBinnedScatterbinnedSmoothingbinnedSmoothing.numericbinnedSmoothing.RawGenomicSignalsbinnedSmoothingByFieldbinnedSmoothingByField.RawGenomicSignalsbinnedSmoothingByStatebinnedSmoothingByState.SegmentedGenomicSignalsInterfacebinnedSumsbinnedSums.RawSequenceReadsbinScatterbinScatter.matrixbyChipTypebyChipType.AromaCellTabularBinaryFilebyChipType.AromaMicroarrayTabularBinaryFilebyChipType.AromaUnitTabularBinaryFilebyChipType.UnitAnnotationDataFilebyGenomebyGenome.AromaGenomeTextFilebyName.AromaPlatformbyName.AromaUnitFracBCnBinarySetbyName.AromaUnitGenotypeCallSetbyName.AromaUnitPscnBinarySetbyName.AromaUnitSignalBinarySetbyName.AromaUnitTotalCnBinarySetbyName.CbsSegmentationDataSetbyPath.AromaMicroarrayDataSetTuplebyPath.AromaUnitCallSetbyPath.AromaUnitGenotypeCallSetbyPath.CbsSegmentationDataSetbyPath.SegmentationDataSetbyPathnamesbyPathnames.SampleAnnotationSetCacheKeyInterfacecalcMarginscalcMargins.matrixcalculateAverageColumnAcrossFilescalculateAverageColumnAcrossFiles.GenericTabularFileSetcalculateChromosomeStatisticscalculateChromosomeStatistics.CopyNumberChromosomalModelcalculateRatioscalculateRatios.CopyNumberChromosomalModelcallNaiveGenotypescallNaiveGenotypes.NonPairedPSCNDatacallNaiveGenotypes.PairedPSCNDatacallSegmentationOutlierscallSegmentationOutliers.NonPairedPSCNDatacallSegmentationOutliers.PairedPSCNDatacallSNPscallSNPs.AbstractPSCNDataCbsModelCbsSegmentationDataFileCbsSegmentationDataSetChromosomalModelChromosomeExplorerclearCache.AromaRepositoryclearCache.RawGenomicSignalsclone.RawGenomicSignalscnRangecnRange.RawCopyNumberscolApplycolApply.AromaTabularBinaryFilecolBinnedSmoothingcolBinnedSmoothing.matrixcolGaussianSmoothingcolGaussianSmoothing.matrixcolKernelSmoothingcolKernelSmoothing.matrixcolMeanscolMeans.AromaTabularBinaryFilecolMeans.defaultcolorizecolorize.Imagecolorize.RasterImagecolStatscolStats.AromaTabularBinaryFilecolSumscolSums.AromaTabularBinaryFilecolSums.defaultconvertTableconvertTable.defaultCopyNumberChromosomalModelCopyNumberDataFileCopyNumberDataSetCopyNumberDataSetTupleCopyNumberOutliersCopyNumberRegionsCopyNumberSegmentationModelcountBasescountBases.AromaCellSequenceFilecountBasesInternalcountBasesInternal.AromaCellSequenceFilecreateImagecreateImage.matrixdim.RichDataFramedimnames<-.AromaTabularBinaryFiledisplaydisplay.ChromosomeExplorerdisplay.Explorerdisplay.Imagedisplay.RasterImagedivideBydivideBy.RawGenomicSignalsdoCBSdoCBS.CopyNumberDataSetdoCBS.CopyNumberDataSetTupledoCBS.defaultdownloadACCdownloadACC.AromaRepositorydownloadACMdownloadACM.AromaRepositorydownloadACPdownloadACP.AromaRepositorydownloadACSdownloadACS.AromaRepositorydownloadAlldownloadAll.AromaRepositorydownloadCDFdownloadCDF.AromaRepositorydownloadChipTypeFiledownloadChipTypeFile.AromaRepositorydownloadFile.AromaRepositorydownloadProbeSeqsTXTdownloadProbeSeqsTXT.AromaRepositorydownloadTXTdownloadTXT.AromaRepositorydownloadUFLdownloadUFL.AromaRepositorydownloadUGCdownloadUGC.AromaRepositorydownloadUGPdownloadUGP.AromaRepositorydrawCnRegionsdrawCnRegions.DNAcopydrawCnRegions.HaarSegdrawCnRegions.MPCBSdrawCnRegions.profileCGHdrawCytobanddrawCytoband.ChromosomalModeldrawCytoband.profileCGHdrawCytoband2drawCytoband2.defaultdrawDensitydrawDensity.CopyNumberRegionsdrawDensity.RawGenomicSignalsdrawExtraAnnotationsdrawExtraAnnotations.defaultdrawExtraAnnotations.profileCGHdrawLevelsdrawLevels.CopyNumberOutliersdrawLevels.CopyNumberRegionsdropAlphadropAlpha.RasterImagedropSegmentationOutliersdropSegmentationOutliers.NonPairedPSCNDatadropSegmentationOutliers.PairedPSCNDatadropVirtualColumndropVirtualColumn.RichDataFrameequals.AromaPlatformequals.CopyNumberRegionsestimateSdsestimateSds.CopyNumberChromosomalModelestimateStandardDeviationestimateStandardDeviation.RawGenomicSignalsExplorerexportAromaUnitPscnBinarySetexportAromaUnitPscnBinarySet.AromaUnitTotalCnBinarySetexportAromaUnitPscnBinarySet.listexportFracBDiffSetexportFracBDiffSet.AromaUnitFracBCnBinarySetexportTotalCnRatioSetexportTotalCnRatioSet.AromaUnitTotalCnBinarySetextractByChromosomeextractByChromosome.AromaUnitChromosomeTabularBinaryFileextractByReferenceNameextractByReferenceName.SegmentationDataSetextractBySampleNameextractBySampleName.SegmentationDataSetextractCallArrayextractCallArray.AromaUnitCallFileextractCallArray.AromaUnitCallSetextractCallsextractCalls.AromaUnitCallFileextractCalls.AromaUnitCallSetextractChromosomeextractChromosome.RawGenomicSignalsextractChromosomesextractChromosomes.RawGenomicSignalsextractCNRsextractCNRs.defaultextractCopyNumberOutliersextractCopyNumberOutliers.DNAcopyextractCopyNumberOutliers.profileCGHextractCopyNumberRegionsextractCopyNumberRegions.defaultextractCopyNumberRegions.DNAcopyextractCopyNumberRegions.HaarSegextractCopyNumberRegions.MPCBSextractCopyNumberRegions.profileCGHextractCopyNumberRegions.SegmentationDataFileextractCopyNumberRegions.SegmentationDataSetextractDataForSegmentationextractDataForSegmentation.RawGenomicSignalsextractGenotypeMatrixextractGenotypeMatrix.AromaUnitCallSetextractGenotypeMatrix.AromaUnitGenotypeCallFileextractGenotypesextractGenotypes.AromaUnitGenotypeCallFileextractGenotypes.AromaUnitGenotypeCallSetextractIGVextractIGV.CopyNumberRegionsextractMatrix.AromaUnitCallFileextractMatrix.AromaUnitSignalBinaryFileextractMergedRawCopyNumbersextractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileListextractNonPairedPSCNDataextractNonPairedPSCNData.PairedPSCNDataextractPSCNArrayextractPSCNArray.AromaUnitTotalCnBinaryFileextractPSCNArray.AromaUnitTotalCnBinarySetextractPSCNMatrixextractPSCNMatrix.AromaUnitTotalCnBinaryFileextractRawAlleleBFractionsextractRawAlleleBFractions.AromaUnitFracBCnBinaryFileextractRawAlleleBFractions.defaultextractRawCNsextractRawCNs.defaultextractRawCopyNumbersextractRawCopyNumbers.AromaUnitPscnBinaryFileextractRawCopyNumbers.AromaUnitTotalCnBinaryFileextractRawCopyNumbers.AromaUnitTotalCnBinaryFileListextractRawCopyNumbers.CopyNumberChromosomalModelextractRawCopyNumbers.defaultextractRawCopyNumbers.DNAcopyextractRawCopyNumbers.HaarSegextractRawCopyNumbers.profileCGHextractRawCopyNumbers.RawCopyNumbersextractRawCopyNumbers.RawSequenceReadsextractRawGenomicSignalsextractRawGenomicSignals.AromaUnitSignalBinaryFileextractRawGenomicSignals.AromaUnitTotalCnBinaryFileListextractRawGenomicSignals.defaultextractRawMirroredAlleleBFractionsextractRawMirroredAlleleBFractions.defaultextractRawMirroredAlleleBFractions.RawAlleleBFractionsextractRegionextractRegion.RawGenomicSignalsextractRegionsextractRegions.RawGenomicSignalsextractSubsetextractSubset.RawGenomicSignalsextractSubsetByStateextractSubsetByState.SegmentedGenomicSignalsInterfaceFileCacheKeyInterfacefindAnnotationDatafindAnnotationData.defaultfindAnnotationDataByChipTypefindAnnotationDataByChipType.AromaRepositoryfindAnnotationDataByChipType.defaultfindByChipTypefindByChipType.AromaMicroarrayTabularBinaryFilefindByChipType.TextUnitNamesFilefindByGenomefindByGenome.AromaGenomeTextFilefindByGenome.AromaUcscGenomeTextFilefindByName.AromaUnitCallSetfindByName.AromaUnitSignalBinarySetfindChangePointsByStatefindChangePointsByState.SegmentedGenomicSignalsInterfacefindFilesTodofindFilesTodo.AromaTransformfindLargeGapsfindLargeGaps.AbstractCNDatafindPngDevicefindPngDevice.defaultfindSAFsfindSAFs.SampleAnnotationSetfindUnitNamesFilefindUnitNamesFile.AromaPlatformfindUnitsTodofindUnitsTodo.AromaUnitCallFilefindUnitsTodo.AromaUnitCallSetfindUnitTypesFilefindUnitTypesFile.AromaPlatformfitfit.ChromosomalModelfit.CopyNumberChromosomalModelfit.CopyNumberSegmentationModelfit2dfit2d.matrixfitGenotypeConefitGenotypeCone.matrixfitGenotypeConeByExpectilefitGenotypeConeByExpectile.matrixfitGenotypeConeBySfitfitGenotypeConeBySfit.matrixfitMultiDimensionalConefitMultiDimensionalCone.matrixfitProbePositionEffectsfitProbePositionEffects.numericfitSplineBlockPolishfitSplineBlockPolish.matrixfitWHLAPLMfitWHLAPLM.matrixfitWHRCModelfitWHRCModel.matrixfitWLAPLMfitWLAPLM.matrixfitWRCModelfitWRCModel.matrixfitWRMAfitWRMA.matrixfixSearchPathfixSearchPath.AromaCorefixSearchPath.AromaPackagefixSearchPathInternalfixSearchPathInternal.AromaPackagefromFile.AromaUnitSignalBinaryFilefromPathfromPath.SampleAnnotationFilefromPath.SampleAnnotationSetgaussianSmoothinggaussianSmoothing.matrixgaussianSmoothing.numericgaussianSmoothing.RawGenomicSignalsgaussKernelgetAliasgetAlias.ChromosomalModelgetAlias.ExplorergetAMgetAM.AromaUnitTotalCnBinaryFilegetAromaFullNameTranslatorSetgetAromaFullNameTranslatorSet.AromaMicroarrayDataSetgetAromaFullNameTranslatorSet.AromaUnitSignalBinarySetgetAromaFullNameTranslatorSet.charactergetAromaGenomeTextFilegetAromaGenomeTextFile.ChromosomalModelgetAromaPlatformgetAromaPlatform.AromaPlatformInterfacegetAromaUflFilegetAromaUflFile.AromaPlatformInterfacegetAromaUflFile.UnitAnnotationDataFilegetAromaUgpFilegetAromaUgpFile.AromaPlatformgetAromaUgpFile.AromaPlatformInterfacegetAromaUgpFile.AromaUnitSignalBinarySetgetAromaUgpFile.UnitAnnotationDataFilegetArraysgetArrays.ChromosomalModelgetArrays.ExplorergetArraysOfInputgetArraysOfInput.ChromosomeExplorergetArraysOfInput.ExplorergetAsteriskTags.AromaMicroarrayDataSetTuplegetAsteriskTags.AromaTransformgetAsteriskTags.ChromosomalModelgetAsteriskTags.CopyNumberSegmentationModelgetAsteriskTags.ExplorergetAsteriskTags.HaarSegModelgetAsteriskTags.RawCopyNumberModelgetAttributeXYgetAttributeXY.AromaMicroarrayDataFilegetAverageFilegetAverageFile.AromaMicroarrayDataSetgetAverageFile.AromaUnitPscnBinarySetgetAverageFile.AromaUnitTotalCnBinarySetgetBasicFieldgetBasicField.RawGenomicSignalsgetBytesPerColumngetBytesPerColumn.AromaTabularBinaryFilegetCacheKeygetCacheKey.CacheKeyInterfacegetCacheKey.FileCacheKeyInterfacegetChipTypegetChipType.AbstractCNDatagetChipType.AromaMicroarrayDataFilegetChipType.AromaMicroarrayDataSetgetChipType.AromaMicroarrayTabularBinaryFilegetChipType.AromaPlatformInterfacegetChipType.AromaUnitSignalBinaryFilegetChipType.AromaUnitSignalBinarySetgetChipType.AromaUnitTypesFilegetChipType.ChromosomalModelgetChipType.SegmentationDataSetgetChipType.TextUnitNamesFilegetChipType.UnitAnnotationDataFilegetChipTypesgetChipTypes.AromaMicroarrayDataSetTuplegetChipTypes.ChromosomalModelgetChromosomegetChromosome.ArgumentsgetChromosome.RawGenomicSignalsgetChromosome.SegmentationDataFilegetChromosomeLabelsgetChromosomeLabels.ChromosomeExplorergetChromosomeLengthgetChromosomeLength.CopyNumberChromosomalModelgetChromosomesgetChromosomes.ArgumentsgetChromosomes.AromaUnitChromosomeTabularBinaryFilegetChromosomes.ChromosomalModelgetChromosomes.ChromosomeExplorergetChromosomes.CopyNumberRegionsgetChromosomes.RawGenomicSignalsgetChromosomes.SegmentationDataSetgetCngetCn.RawCopyNumbersgetCNsgetCNs.RawCopyNumbersgetColClassesgetColClasses.AromaTabularBinaryFilegetColumnNames.RichDataFramegetColumnNamesTranslator.RichDataFramegetCommonListElementsgetCXYgetCXY.RawGenomicSignalsgetDataFileMatrixgetDataFileMatrix.CopyNumberChromosomalModelgetDefaultColumnNames.AromaCellCpgFilegetDefaultColumnNames.AromaCellPositionFilegetDefaultColumnNames.AromaCellSequenceFilegetDefaultColumnNames.AromaTabularBinaryFilegetDefaultColumnNames.AromaUflFilegetDefaultColumnNames.AromaUgpFilegetDefaultColumnNames.AromaUnitChromosomeTabularBinaryFilegetDefaultColumnNames.AromaUnitGcContentFilegetDefaultColumnNames.AromaUnitPscnBinaryFilegetDefaultExtensiongetDefaultExtension.AromaCellCpgFilegetDefaultExtension.AromaCellPositionFilegetDefaultExtension.AromaCellSequenceFilegetDefaultExtension.AromaUflFilegetDefaultExtension.AromaUgpFilegetDefaultExtension.UnitAnnotationDataFilegetDefaultFullName.AromaMicroarrayDataSetgetDefaultFullName.AromaTabularBinarySetgetDefaultFullName.SegmentationDataSetgetDefaultLocusFieldsgetDefaultLocusFields.RawGenomicSignalsgetDensitygetDensity.CopyNumberRegionsgetDeviceResolutiongetDeviceResolution.defaultgetEffectsgetEffects.ProbePositionEffectsgetExpectedOutputFilesgetExpectedOutputFiles.AromaTransformgetExpectedOutputFullnamesgetExpectedOutputFullnames.AromaTransformgetExtensionPattern.AromaCellPositionFilegetExtensionPattern.AromaCellSequenceFilegetExtensionPattern.AromaUflFilegetExtensionPattern.AromaUgpFilegetExtensionPattern.AromaUnitGcContentFilegetExtensionPattern.AromaUnitSignalBinaryFilegetExtensionPattern.SampleAnnotationFilegetExtensionPattern.TextUnitNamesFilegetFilenameExtension.AromaCellCpgFilegetFilenameExtension.AromaCellPositionFilegetFilenameExtension.AromaCellSequenceFilegetFilenameExtension.AromaMicroarrayTabularBinaryFilegetFilenameExtension.AromaUflFilegetFilenameExtension.AromaUgpFilegetFilenameExtension.AromaUnitChromosomeTabularBinaryFilegetFilenameExtension.AromaUnitGcContentFilegetFilenameExtension.AromaUnitSignalBinaryFilegetFilenameExtension.TextUnitNamesFilegetFitFunctiongetFitFunction.CbsModelgetFitFunction.CopyNumberSegmentationModelgetFitFunction.GladModelgetFitFunction.HaarSegModelgetFullName.AromaTransformgetFullName.ChromosomalModelgetFullName.ExplorergetFullName.RichDataFramegetFullNames.AromaMicroarrayDataSetTuplegetFullNames.ChromosomalModelgetFullNames.ChromosomeExplorergetFullNames.CopyNumberSegmentationModelgetFullNameTranslatorSetgetFullNameTranslatorSet.charactergetFullNameTranslatorSet.GenericDataFileSetgetGenericSummarygetGenericSummary.RichDataFramegetGenomegetGenome.ChromosomalModelgetGenomeDatagetGenomeData.ChromosomalModelgetGenomeFilegetGenomeFile.ChromosomalModelgetGenomeVersiongetGenomeVersion.AromaUnitChromosomeTabularBinaryFilegetImagegetImage.matrixgetImageDatagetImageData.ImagegetImageData.RasterImagegetIncludePathgetIncludePath.ExplorergetInputDataSetgetInputDataSet.AromaTransformgetLengthgetLength.CopyNumberRegionsgetListOfAromaUgpFilesgetListOfAromaUgpFiles.ChromosomalModelgetListOfUnitNamesFilesgetListOfUnitNamesFiles.AromaUnitTotalCnBinarySetTuplegetListOfUnitNamesFiles.ChromosomalModelgetListOfUnitTypesFilesgetListOfUnitTypesFiles.ChromosomalModelgetLocusDatagetLocusData.AbstractCNDatagetLocusFieldsgetLocusFields.RawGenomicSignalsgetLog2RatiosgetLog2Ratios.CopyNumberSegmentationModelgetMainPathgetMainPath.ExplorergetMaxLengthRepeatsgetMaxLengthRepeats.AromaCellSequenceFilegetMaxNAFractiongetMaxNAFraction.CopyNumberChromosomalModelgetMeanAtgetMeanAt.CopyNumberRegionsgetModelgetModel.ChromosomeExplorergetName.AromaPlatformgetName.AromaTransformgetName.ChromosomalModelgetName.ExplorergetName.RichDataFramegetNameOfInputgetNameOfInput.ChromosomeExplorergetNameOfInput.ExplorergetNames.ChromosomalModelgetNames.ChromosomeExplorergetNames.CopyNumberChromosomalModelgetNames.ExplorergetNumberOfFilesAveragedgetNumberOfFilesAveraged.AromaUnitSignalBinaryFilegetNumberOfFilesAveraged.CopyNumberDataFilegetOptionalArgumentsgetOptionalArguments.CopyNumberChromosomalModelgetOutputDataSetgetOutputDataSet.AromaTransformgetOutputDataSet0getOutputDataSet0.AromaTransformgetOutputFilesgetOutputFiles.AromaTransformgetOutputSetgetOutputSet.ChromosomalModelgetPairedNamesgetPairedNames.CopyNumberChromosomalModelgetParametersgetParameters.ParametersInterfacegetParametersAsStringgetParametersAsString.ParametersInterfacegetParameterSetsgetParameterSets.ParametersInterfacegetParentNamegetParentName.GenericDataFilegetParentName.GenericDataFileSetgetParentPathgetParentPath.ChromosomalModelgetPath.AromaTransformgetPath.ChromosomalModelgetPath.ChromosomeExplorergetPath.ExplorergetPatternsgetPatterns.SampleAnnotationFilegetPlatformgetPlatform.AbstractCNDatagetPlatform.AromaMicroarrayDataFilegetPlatform.AromaMicroarrayDataSetgetPlatform.AromaMicroarrayTabularBinaryFilegetPlatform.AromaPlatformInterfacegetPlatform.AromaUnitSignalBinaryFilegetPlatform.AromaUnitSignalBinarySetgetPlatform.AromaUnitTypesFilegetPlatform.TextUnitNamesFilegetPlatform.UnitAnnotationDataFilegetPloidygetPloidy.AromaMicroarrayDataFilegetPositionsgetPositions.AromaUgpFilegetPositions.RawGenomicSignalsgetProbeLengthgetProbeLength.AromaCellSequenceFilegetProbePositionEffectDesignMatrixgetProbePositionEffectDesignMatrix.charactergetProbePositionEffectDesignMatrix.rawgetRamgetRam.AromaSettingsgetRandomSeedgetRandomSeed.CbsModelgetRawCnDatagetRawCnData.CopyNumberChromosomalModelgetReferencegetReference.CopyNumberChromosomalModelgetReferenceNamegetReferenceName.SegmentationDataFilegetReferenceNamesgetReferenceNames.SegmentationDataSetgetReferenceSetTuplegetReferenceSetTuple.CopyNumberChromosomalModelgetRefSetTuplegetRefSetTuple.CopyNumberChromosomalModelgetRegionsgetRegions.CopyNumberSegmentationModelgetReportPathgetReportPath.ChromosomalModelgetReportPathPatterngetReportPathPattern.ExplorergetRootNamegetRootName.AromaTabularBinaryFilegetRootName.AromaTabularBinarySetgetRootPathgetRootPath.AromaTransformgetRootPath.ChromosomalModelgetRootPath.ExplorergetSampleLabelsgetSampleLabels.ChromosomeExplorergetSampleLayerNamegetSampleLayerName.ExplorergetSampleLayerPrefixgetSampleLayerPrefix.ExplorergetSampleNamegetSampleName.SegmentationDataFilegetSampleNamesgetSampleNames.SegmentationDataSetgetSets.AromaMicroarrayDataSetTuplegetSets.ChromosomalModelgetSetTaggetSetTag.ChromosomalModelgetSetTag.RawCopyNumberModelgetSetTuplegetSetTuple.ChromosomalModelgetSigmagetSigma.RawGenomicSignalsgetSignalColumnNamegetSignalColumnName.RawGenomicSignalsgetSignalColumnNamesgetSignalColumnNames.NonPairedPSCNDatagetSignalColumnNames.PairedPSCNDatagetSignalColumnNames.RawGenomicSignalsgetSignalsgetSignals.RawCopyNumbersgetSignals.RawGenomicSignalsgetSNPFieldsgetSNPFields.AbstractPSCNDatagetSnpNucleotidesgetSnpNucleotides.AromaCellSequenceFilegetSnpPositionsgetSnpPositions.AromaCellSequenceFilegetSnpShiftsgetSnpShifts.AromaCellSequenceFilegetStateColorMapgetStateColorMap.SegmentedGenomicSignalsInterfacegetStateColorsgetStateColors.SegmentedGenomicSignalsInterfacegetStatesgetStates.SegmentedGenomicSignalsInterfacegetSubnamegetSubname.ExplorergetTableOfArraysgetTableOfArrays.ChromosomalModelgetTags.AromaMicroarrayDataSetTuplegetTags.AromaTransformgetTags.ChromosomalModelgetTags.CopyNumberSegmentationModelgetTags.ExplorergetTags.RichDataFramegetTagsOfInputgetTagsOfInput.ChromosomeExplorergetTagsOfInput.ExplorergetTCNsgetTCNs.PairedPSCNDatagetTemplatePathgetTemplatePath.ExplorergetTotalCopyNumbersgetTotalCopyNumbers.PairedPSCNDatagetUniqueStatesgetUniqueStates.SegmentedGenomicSignalsInterfacegetUnitAnnotationDataFilegetUnitAnnotationDataFile.AromaPlatformInterfacegetUnitNamesgetUnitNames.TextUnitNamesFilegetUnitNames.UnitNamesFilegetUnitNamesFilegetUnitNamesFile.AromaPlatformgetUnitNamesFile.AromaPlatformInterfacegetUnitNamesFile.AromaUnitTotalCnBinarySetgetUnitsAtgetUnitsAt.AromaUgpFilegetUnitsOnChromosomegetUnitsOnChromosome.AromaUgpFilegetUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFilegetUnitsOnChromosomesgetUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFilegetUnitTypesgetUnitTypes.AromaUnitTypesFilegetUnitTypes.UnitTypesFilegetUnitTypesFilegetUnitTypesFile.AromaPlatformgetUnitTypesFile.AromaPlatformInterfacegetUrlPathgetUrlPath.AromaRepositorygetValueAtgetValueAt.CopyNumberRegionsgetVerbose.AromaRepositorygetVerbose.AromaSettingsgetVersion.ExplorergetVirtualColumngetVirtualColumn.RichDataFramegetVirtualColumnFunctiongetVirtualColumnFunction.RichDataFramegetVirtualColumnFunctionsgetVirtualColumnFunctions.RichDataFramegetVirtualColumnNamesgetVirtualColumnNames.RichDataFramegetVirtualFieldgetVirtualField.SegmentedGenomicSignalsInterfacegetVirtualLocusFieldsgetVirtualLocusFields.SegmentedGenomicSignalsInterfacegetWeightsgetWeights.RawGenomicSignalsgetXAMgetXAM.AromaMicroarrayDataFilegetXAM.AromaUnitTotalCnBinaryFilegetXScalegetXScale.RawGenomicSignalsgetXYgetXY.RawGenomicSignalsgetYScalegetYScale.RawGenomicSignalsgetZoomsgetZooms.ChromosomeExplorerGladModelgroupBySnpNucleotidesgroupBySnpNucleotides.AromaCellSequenceFileHaarSegModelhasAlleleBFractionshasAlleleBFractions.AromaUnitPscnBinaryFilehasAlleleBFractions.AromaUnitTotalCnBinaryFilehasAlleleBFractions.CopyNumberDataFilehasAlleleBFractions.CopyNumberDataSethasAlleleBFractions.CopyNumberDataSetTuplehasAttributeXYhasAttributeXY.AromaMicroarrayDataFilehasColumnhasColumn.RichDataFramehasColumnshasColumns.RichDataFramehasKnownPositionshasKnownPositions.AbstractCNDatahasStrandinesshasStrandiness.AromaUnitPscnBinaryFilehasStrandiness.AromaUnitTotalCnBinaryFilehasStrandiness.CopyNumberDataFilehasStrandiness.CopyNumberDataSethasStrandiness.CopyNumberDataSetTuplehasTotalCopyNumberRatioshasTotalCopyNumberRatios.AromaUnitPscnBinaryFilehasVirtualColumnhasVirtualColumn.RichDataFramehasVirtualColumnshasVirtualColumns.RichDataFramehasWeightshasWeights.RawGenomicSignalsimportFromimportFrom.AromaTabularBinaryFileimportFromGenericTabularFileimportFromGenericTabularFile.AromaUflFileimportFromGenericTabularFile.AromaUgpFileimportFromUnitTypesFileimportFromUnitTypesFile.AromaUnitTypesFileindexOf.AromaMicroarrayDataSetTupleindexOf.ChromosomalModelindexOf.ChromosomeExplorerindexOf.UnitNamesFileindexOfColumnindexOfColumn.AromaUnitChromosomeTabularBinaryFileindexOfUnitsindexOfUnits.AromaUnitTabularBinaryFileinterleaveinterleave.Imageinterleave.RasterImageisAverageFileisAverageFile.AromaMicroarrayDataFileisAverageFile.AromaUnitSignalBinaryFileisCompatibleWithisCompatibleWith.AromaPlatformInterfaceisDone.AromaTransformisHeterozygousisHeterozygous.AromaUnitGenotypeCallFileisHomozygousisHomozygous.AromaUnitGenotypeCallFileisMissingisMissing.AromaCellCpgFileisMissing.AromaCellPositionFileisMissing.AromaCellSequenceFileisPairedisPaired.CopyNumberChromosomalModelkernelSmoothingkernelSmoothing.numerickernelSmoothing.RawGenomicSignalskernelSmoothingByStatekernelSmoothingByState.SegmentedGenomicSignalsInterfacelapplyInChunkslapplyInChunks.numericlength.RichDataFramelibrarylines.CopyNumberOutlierslines.CopyNumberRegionslines.RawGenomicSignalslistFileslistFiles.AromaRepositorylistToXmllistToXml.listloadAllloadAll.SampleAnnotationSetloadFitloadFit.CbsSegmentationDataFileloadFit.SegmentationDataFilelocallyUniquelocallyUnique.defaultlog2abslog2centerlog2neglog2posmatchPatternsmatchPatterns.SampleAnnotationFilematrixBlockPolishmatrixBlockPolish.matrixmergeBoxplotStatsmergeBoxplotStats.listmultiplyBymultiplyBy.RawGenomicSignalsnames.RichDataFramenbrOfArraysnbrOfArrays.ChromosomalModelnbrOfArrays.ExplorernbrOfCellsnbrOfCells.AromaCellTabularBinaryFilenbrOfChipTypesnbrOfChipTypes.AromaMicroarrayDataSetTuplenbrOfChipTypes.ChromosomalModelnbrOfChromosomesnbrOfChromosomes.CopyNumberRegionsnbrOfChromosomes.RawGenomicSignalsnbrOfColumns.AromaTabularBinaryFilenbrOfEnzymesnbrOfEnzymes.AromaUflFilenbrOfLocinbrOfLoci.RawGenomicSignalsnbrOfReadsnbrOfReads.RawSequenceReadsnbrOfRegionsnbrOfRegions.CopyNumberOutliersnbrOfRegions.CopyNumberRegionsnbrOfRows.AromaTabularBinaryFilenbrOfUnitsnbrOfUnits.AromaUnitSignalBinaryFilenbrOfUnits.AromaUnitTabularBinaryFilenbrOfUnits.TextUnitNamesFilenbrOfUnits.UnitAnnotationDataFilenbrOfUnits.UnitNamesFilenbrOfUnits.UnitTypesFilenewInstance.RichDataFramenewPlotnewPlot.CopyNumberChromosomalModelNonPairedPSCNDatanorm2dnorm2d.matrixnormalizeGenotypeConenormalizeGenotypeCone.matrixnormalizeTumorBoostnormalizeTumorBoost.PairedPSCNDataonFitAddGenotypeCallsonFitAddGenotypeCalls.defaultonFitAddGenotypeCalls.GladModelorderAlongGenomeorderAlongGenome.AbstractCNDataPairedPSCNDataParametersInterfaceplot.BinnedScatterplot.CopyNumberSegmentationModelplot.ProbePositionEffectsplot.RawAlleleBFractionsplot.RawCopyNumbersplot.RawGenomicSignalsplot.RawMirroredAlleleBFractionsplot.RawSequenceReadsplot.SegmentedGenomicSignalsInterfaceplotAxesLayersplotAxesLayers.CopyNumberChromosomalModelplotChromosomesLayersplotChromosomesLayers.CopyNumberChromosomalModelplotCopyNumberRegionLayersplotCopyNumberRegionLayers.CopyNumberSegmentationModelplotCoverageMapplotCoverageMap.AromaUgpFileplotCytobandLayersplotCytobandLayers.CopyNumberChromosomalModelplotFitLayersplotFitLayers.CopyNumberChromosomalModelplotGridHorizontalLayersplotGridHorizontalLayers.CopyNumberChromosomalModelplotProfile2plotProfile2.profileCGHplotRawCNsplotRawCNs.profileCGHplotRawCopyNumbersplotRawCopyNumbers.CopyNumberChromosomalModelplotSampleLayersplotSampleLayers.CopyNumberChromosomalModelplotTracksplotTracks.PairedPSCNDatapoints.BinnedScatterpoints.RawGenomicSignalspoints.SegmentedGenomicSignalsInterfacepointsRawCNspointsRawCNs.defaultpointsRawCNs.profileCGHpointsSequencepointsSequence.ProbePositionEffectspredict.ProbePositionEffectsprint.RawGenomicSignalsprint.RichDataFrameprocessprocess.AromaTransformprocess.ChromosomeExplorerprocess.ExplorerprocessTimeprocessTime.defaultpruneprune.CopyNumberRegionsRasterImageRawAlleleBFractionsRawCopyNumberModelRawCopyNumbersRawGenomicSignalsRawMirroredAlleleBFractionsRawSequenceReadsrbind.RichDataFramereadread.RasterImagereadColumns.AromaTabularBinaryFilereadCpgsreadCpgs.AromaCellCpgFilereadDataFrame.AromaGenomeTextFilereadDataFrame.AromaTabularBinaryFilereadDataFrame.AromaUcscGenomeTextFilereadDataFrame.AromaUflFilereadDataFrame.AromaUnitChromosomeTabularBinaryFilereadDataFrame.AromaUnitSignalBinaryFilereadDataFrame.SampleAnnotationFilereadFooterreadFooter.AromaTabularBinaryFilereadHeaderreadHeader.AromaTabularBinaryFilereadNeighborSequenceMatrixreadNeighborSequenceMatrix.AromaCellSequenceFilereadPairSequenceMatrixreadPairSequenceMatrix.AromaCellSequenceFilereadPositionsreadPositions.AromaCellPositionFilereadRawFooterreadRawFooter.AromaTabularBinaryFilereadSequenceMatrixreadSequenceMatrix.AromaCellSequenceFilereadSequencesreadSequences.AromaCellSequenceFilereadTargetStrandsreadTargetStrands.AromaCellSequenceFileremapremap.defaultreorder.BinnedScatterrequirerequireWithMemoryrequireWithMemory.defaultrescalerescale.Imagerescale.RasterImageRichDataFrameSampleAnnotationFileSampleAnnotationSetsave.RasterImageSegmentationDataFileSegmentationDataSetsegmentByCBSsegmentByCBS.NonPairedPSCNDatasegmentByCBS.PairedPSCNDatasegmentByCBS.RawGenomicSignalssegmentByGLADsegmentByGLAD.RawGenomicSignalssegmentByHaarSegsegmentByHaarSeg.RawGenomicSignalssegmentByMPCBSsegmentByMPCBS.RawGenomicSignalssegmentByPairedPSCBSsegmentByPairedPSCBS.PairedPSCNDataSegmentedAlleleBFractionsSegmentedCopyNumbersSegmentedGenomicSignalsInterfacesetAliassetAlias.ExplorersetArrayssetArrays.ChromosomeExplorersetArrays.ExplorersetAttributes.RichDataFramesetAttributesBy.AromaMicroarrayDataSetsetAttributesBy.AromaTabularBinarySetsetAttributesBySampleAnnotationFilesetAttributesBySampleAnnotationFile.AromaMicroarrayDataSetsetAttributesBySampleAnnotationFile.AromaTabularBinarySetsetAttributesBySampleAnnotationSetsetAttributesBySampleAnnotationSet.AromaMicroarrayDataSetsetAttributesBySampleAnnotationSet.AromaTabularBinarySetsetAttributesByTags.AromaMicroarrayDataFilesetAttributesByTags.AromaTabularBinaryFilesetAttributesByTags.AromaTabularBinarySetsetAttributeXYsetAttributeXY.AromaMicroarrayDataFilesetBasicFieldsetBasicField.RawGenomicSignalssetChipTypesetChipType.AbstractCNDatasetChromosomessetChromosomes.ChromosomalModelsetColumnNamesMapsetColumnNamesMap.RichDataFramesetColumnNamesTranslator.RichDataFramesetCytobandsetCytoband.ChromosomeExplorersetGenomesetGenome.ChromosomalModelsetImageDatasetImageData.ImagesetImageData.RasterImagesetName.RichDataFramesetPlatformsetPlatform.AbstractCNDatasetRamsetRam.AromaSettingssetRandomSeedsetRandomSeed.CbsModelsetReferencesetReference.CopyNumberChromosomalModelsetReportPathPatternsetReportPathPattern.ExplorersetSigmasetSigma.RawGenomicSignalssetSignalssetSignals.RawGenomicSignalssetStateColorMapsetStateColorMap.SegmentedGenomicSignalsInterfacesetStatessetStates.SegmentedGenomicSignalsInterfacesetSubnamesetSubname.ExplorersetTags.AromaTransformsetTags.RichDataFramesetupsetup.ExplorersetVerbosesetVerbose.AromaRepositorysetVerbose.AromaSettingssetVirtualColumnsetVirtualColumn.RichDataFramesetVirtualColumnFunctionssetVirtualColumnFunctions.RichDataFramesetWeightssetWeights.RawGenomicSignalssetXScalesetXScale.RawGenomicSignalssetYScalesetYScale.RawGenomicSignalssetZoomssetZooms.ChromosomeExplorershakyTextshakyText.defaultsignalRangesignalRange.RawGenomicSignalssimulateRawCopyNumberssimulateRawCopyNumbers.CopyNumberRegionssmoothWRMAsmoothWRMA.matrixsmoothWSAsmoothWSA.matrixsort.RawGenomicSignalssplitByReportPathPatternsplitByReportPathPattern.ExplorersplitInChunkssplitInChunks.numericsqrtabssqrtcentersqrtnegsqrtpossqrtsignstextChipTypestextChipType.characterstextLabelstextLabel.AromaMicroarrayDataFilestextLabelsstextLabels.AromaMicroarrayDataFilestextSizestextSize.AromaMicroarrayDataFilestr.RasterImagestringTreestringTree.charactersubsamplesubsample.BinnedScattersubset.AromaTabularBinaryFilesubset.BinnedScattersubset.CopyNumberRegionssubset.RichDataFramesubtractBysubtractBy.RawGenomicSignalssummary.AromaTabularBinaryFilesummaryOfUnitssummaryOfUnits.AromaUflFiletext.ProbePositionEffectstextSequencetextSequence.ProbePositionEffectsTextUnitNamesFiletranslateColumnNames.RichDataFrameunique.CopyNumberRegionsUnitAnnotationDataFileUnitNamesFileUnitTypesFileupdateCpgsupdateCpgs.AromaCellCpgFileupdateDataupdateData.AromaTabularBinaryFileupdateDataColumnupdateDataColumn.AromaTabularBinaryFileupdateGenotypesupdateGenotypes.AromaUnitGenotypeCallFileupdatePositionsupdatePositions.AromaCellPositionFileupdateSequenceMatrixupdateSequenceMatrix.AromaCellSequenceFileupdateSequencesupdateSequences.AromaCellSequenceFileupdateSetupExplorerFileupdateSetupExplorerFile.ChromosomeExplorerupdateSetupExplorerFile.ExplorerupdateTargetStrandsupdateTargetStrands.AromaCellSequenceFilevalidate.AromaMicroarrayDataSetvalidate.AromaUnitSignalBinarySetwritewrite.defaultwrite.RasterImagewriteAxesLayerswriteAxesLayers.ChromosomeExplorerwriteCopyNumberRegionLayerswriteCopyNumberRegionLayers.ChromosomeExplorerwriteCytobandLayerswriteCytobandLayers.ChromosomeExplorerwriteDataFrame.AromaUnitFracBCnBinarySetwriteDataFrame.AromaUnitPscnBinarySetwriteDataFrame.AromaUnitSignalBinaryFilewriteDataFrame.AromaUnitSignalBinarySetwriteDataFrame.AromaUnitTabularBinaryFilewriteDataFrame.AromaUnitTotalCnBinarySetwriteFooterwriteFooter.AromaTabularBinaryFilewriteGraphswriteGraphs.ChromosomeExplorerwriteGridHorizontalLayerswriteGridHorizontalLayers.ChromosomeExplorerwriteImagewriteImage.ImagewriteImage.RasterImagewriteRawCopyNumberLayerswriteRawCopyNumberLayers.ChromosomeExplorerwriteRawFooterwriteRawFooter.AromaTabularBinaryFilewriteRegionswriteRegions.ChromosomeExplorerwriteRegions.CopyNumberSegmentationModelwriteRegions.GladModelxMaxxMax.CopyNumberRegionsxMax.RawGenomicSignalsxMinxMin.CopyNumberRegionsxMin.RawGenomicSignalsxmlToListxmlToList.characterxRangexRange.CopyNumberRegionsxRange.RawGenomicSignalsxSeqxSeq.RawGenomicSignalsyellow.colorsyMaxyMax.RawGenomicSignalsyMinyMin.RawGenomicSignalsyRangeyRange.RawGenomicSignals
Dependencies:aroma.lightbase64encBiocManagercodetoolsdigestDNAcopyfutureglobalslistenvmatrixStatsparallellyPSCBSR.cacheR.devicesR.filesetsR.methodsS3R.ooR.rspR.utilsRColorBrewer
