Entry: AromaCellTabularBinaryFile
Aliases: AromaCellTabularBinaryFile
Keywords: classes
Description: The AromaCellTabularBinaryFile class
URL: ../../../library/aroma.core/html/AromaCellTabularBinaryFile.html

Entry: AromaMicroarrayDataFile
Aliases: AromaMicroarrayDataFile
Keywords: classes
Description: The abstract AromaMicroarrayDataFile class
URL: ../../../library/aroma.core/html/AromaMicroarrayDataFile.html

Entry: AromaMicroarrayDataSet
Aliases: AromaMicroarrayDataSet
Keywords: classes
Description: The AromaMicroarrayDataSet class
URL: ../../../library/aroma.core/html/AromaMicroarrayDataSet.html

Entry: AromaMicroarrayDataSetTuple
Aliases: AromaMicroarrayDataSetTuple
Keywords: internal methods classes
Description: The AromaMicroarrayDataSetTuple class
URL: ../../../library/aroma.core/html/AromaMicroarrayDataSetTuple.html

Entry: AromaMicroarrayTabularBinaryFile
Aliases: AromaMicroarrayTabularBinaryFile
Keywords: classes
Description: The AromaMicroarrayTabularBinaryFile class
URL: ../../../library/aroma.core/html/AromaMicroarrayTabularBinaryFile.html

Entry: AromaPlatform
Aliases: AromaPlatform
Keywords: classes
Description: The AromaPlatform class
URL: ../../../library/aroma.core/html/AromaPlatform.html

Entry: AromaTabularBinaryFile
Aliases: AromaTabularBinaryFile
Keywords: classes
Description: The AromaTabularBinaryFile class
URL: ../../../library/aroma.core/html/AromaTabularBinaryFile.html

Entry: AromaTabularBinarySet
Aliases: AromaTabularBinarySet
Keywords: classes
Description: The AromaTabularBinarySet class
URL: ../../../library/aroma.core/html/AromaTabularBinarySet.html

Entry: AromaTransform
Aliases: AromaTransform
Keywords: classes
Description: The AromaTransform class
URL: ../../../library/aroma.core/html/AromaTransform.html

Entry: AromaUnitCallFile
Aliases: AromaUnitCallFile
Keywords: classes
Description: The AromaUnitCallFile class
URL: ../../../library/aroma.core/html/AromaUnitCallFile.html

Entry: AromaUnitCallSet
Aliases: AromaUnitCallSet
Keywords: classes
Description: The AromaUnitCallSet class
URL: ../../../library/aroma.core/html/AromaUnitCallSet.html

Entry: AromaUnitFracBCnBinaryFile
Aliases: AromaUnitFracBCnBinaryFile
Keywords: classes
Description: The AromaUnitFracBCnBinaryFile class
URL: ../../../library/aroma.core/html/AromaUnitFracBCnBinaryFile.html

Entry: AromaUnitFracBCnBinarySet
Aliases: AromaUnitFracBCnBinarySet
Keywords: classes
Description: The AromaUnitFracBCnBinarySet class
URL: ../../../library/aroma.core/html/AromaUnitFracBCnBinarySet.html

Entry: AromaUnitGenotypeCallFile
Aliases: AromaUnitGenotypeCallFile
Keywords: classes
Description: The AromaUnitGenotypeCallFile class
URL: ../../../library/aroma.core/html/AromaUnitGenotypeCallFile.html

Entry: AromaUnitGenotypeCallSet
Aliases: AromaUnitGenotypeCallSet
Keywords: classes
Description: The AromaUnitGenotypeCallSet class
URL: ../../../library/aroma.core/html/AromaUnitGenotypeCallSet.html

Entry: AromaUnitSignalBinaryFile
Aliases: AromaUnitSignalBinaryFile
Keywords: classes
Description: The AromaUnitSignalBinaryFile class
URL: ../../../library/aroma.core/html/AromaUnitSignalBinaryFile.html

Entry: AromaUnitSignalBinarySet
Aliases: AromaUnitSignalBinarySet
Keywords: classes
Description: The AromaUnitSignalBinarySet class
URL: ../../../library/aroma.core/html/AromaUnitSignalBinarySet.html

Entry: AromaUnitTabularBinaryFile
Aliases: AromaUnitTabularBinaryFile
Keywords: classes
Description: The AromaUnitTabularBinaryFile class
URL: ../../../library/aroma.core/html/AromaUnitTabularBinaryFile.html

Entry: AromaUnitTotalCnBinaryFile
Aliases: AromaUnitTotalCnBinaryFile
Keywords: classes
Description: The AromaUnitTotalCnBinaryFile class
URL: ../../../library/aroma.core/html/AromaUnitTotalCnBinaryFile.html

Entry: AromaUnitTotalCnBinarySet
Aliases: AromaUnitTotalCnBinarySet
Keywords: classes
Description: The AromaUnitTotalCnBinarySet class
URL: ../../../library/aroma.core/html/AromaUnitTotalCnBinarySet.html

Entry: AromaUnitTypesFile
Aliases: AromaUnitTypesFile
Keywords: classes
Description: The AromaUnitTypesFile class
URL: ../../../library/aroma.core/html/AromaUnitTypesFile.html

Entry: BinnedScatter
Aliases: BinnedScatter
Keywords: classes
Description: The BinnedScatter class
URL: ../../../library/aroma.core/html/BinnedScatter.html

Entry: CbsModel
Aliases: CbsModel
Keywords: classes
Description: The CbsModel class
URL: ../../../library/aroma.core/html/CbsModel.html

Entry: ChromosomalModel
Aliases: ChromosomalModel
Keywords: classes
Description: The ChromosomalModel class
URL: ../../../library/aroma.core/html/ChromosomalModel.html

Entry: ChromosomeExplorer
Aliases: ChromosomeExplorer
Keywords: classes
Description: The ChromosomeExplorer class
URL: ../../../library/aroma.core/html/ChromosomeExplorer.html

Entry: CopyNumberChromosomalModel
Aliases: CopyNumberChromosomalModel
Keywords: classes
Description: The CopyNumberChromosomalModel class
URL: ../../../library/aroma.core/html/CopyNumberChromosomalModel.html

Entry: CopyNumberSegmentationModel
Aliases: CopyNumberSegmentationModel
Keywords: classes
Description: The CopyNumberSegmentationModel class
URL: ../../../library/aroma.core/html/CopyNumberSegmentationModel.html

Entry: Explorer
Aliases: Explorer
Keywords: classes
Description: The Explorer class
URL: ../../../library/aroma.core/html/Explorer.html

Entry: GladModel
Aliases: GladModel
Keywords: classes
Description: The GladModel class
URL: ../../../library/aroma.core/html/GladModel.html

Entry: HaarSegModel
Aliases: HaarSegModel
Keywords: classes
Description: The HaarSegModel class
URL: ../../../library/aroma.core/html/HaarSegModel.html

Entry: Non-documented objects
Aliases: Non-documented objects [.AromaTabularBinaryFile [[.AromaTabularBinaryFile [<-.AromaTabularBinaryFile addBy addBy.RawGenomicSignals addIncludes addIncludes.Explorer addIndexFile addIndexFile.ChromosomeExplorer addIndexFile.Explorer addLocusFields addLocusFields.RawGenomicSignals allocate allocate.AromaCellPositionFile allocate.AromaCellSequenceFile allocate.AromaMicroarrayTabularBinaryFile allocate.AromaUflFile allocate.AromaUgpFile allocate.AromaUnitCallFile allocate.AromaUnitChromosomeTabularBinaryFile allocate.AromaUnitGenotypeCallFile allocate.AromaUnitSignalBinaryFile allocate.AromaUnitTypesFile allocateFromUnitAnnotationDataFile allocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFile allocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFile allocateFromUnitNamesFile allocateFromUnitNamesFile.AromaUnitSignalBinaryFile allocateFromUnitNamesFile.AromaUnitTabularBinaryFile append.RawGenomicSignals apply apply.default apply.SampleAnnotationFile applyBinaryOperator applyBinaryOperator.RawGenomicSignals applyRegions applyRegions.CopyNumberOutliers applyRows applyRows.CopyNumberRegions AromaCellPositionFile AromaCellSequenceFile AromaCore AromaPackage AromaPlatformInterface aromaSettings AromaSettings AromaUflFile AromaUgpFile AromaUnitChromosomeTabularBinaryFile AromaUnitTotalCnBinaryFileList AromaUnitTotalCnBinarySetTuple as.AromaMicroarrayDataSetList as.AromaMicroarrayDataSetList.AromaMicroarrayDataSet as.AromaMicroarrayDataSetTuple as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSet as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetTuple as.AromaUnitTotalCnBinarySetTuple as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySet as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetTuple as.character.AromaMicroarrayDataSetTuple as.character.AromaMicroarrayTabularBinaryFile as.character.AromaTabularBinaryFile as.character.AromaTransform as.character.AromaUnitSignalBinaryFile as.character.ChromosomalModel as.character.ChromosomeExplorer as.character.CopyNumberChromosomalModel as.character.CopyNumberOutliers as.character.CopyNumberRegions as.character.Explorer as.character.RawGenomicSignals as.character.TextUnitNamesFile as.CopyNumberDataFile as.CopyNumberDataFile.CopyNumberDataFile as.CopyNumberDataSet as.CopyNumberDataSet.CopyNumberDataSet as.CopyNumberDataSetTuple as.CopyNumberDataSetTuple.AromaUnitTotalCnBinarySet as.CopyNumberDataSetTuple.CopyNumberDataSetTuple as.CopyNumberDataSetTuple.list as.data.frame.CopyNumberOutliers as.data.frame.CopyNumberRegions as.data.frame.RawCopyNumbers as.data.frame.RawGenomicSignals as.data.frame.SegmentedGenomicSignalsInterface as.GrayscaleImage as.TrueColorImage as.TrueColorImage.Image as.TrueColorImage.matrix asMatrixOfFiles asMatrixOfFiles.AromaMicroarrayDataSetTuple asThis asThis.BasicObject asThis.Object backtransformGenotypeCone backtransformGenotypeCone.matrix backtransformMultiDimensionalCone backtransformMultiDimensionalCone.matrix barSequence barSequence.ProbePositionEffects binnedSmoothing.RawGenomicSignals binnedSmoothingByState binnedSmoothingByState.SegmentedGenomicSignalsInterface binnedSums binnedSums.RawSequenceReads binScatter binScatter.matrix byChipType byChipType.AromaCellPositionFile byChipType.AromaMicroarrayTabularBinaryFile byChipType.AromaUnitTabularBinaryFile byChipType.UnitAnnotationDataFile byName.AromaPlatform byName.AromaUnitFracBCnBinarySet byName.AromaUnitGenotypeCallSet byName.AromaUnitSignalBinarySet byName.AromaUnitTotalCnBinarySet byPath.AromaMicroarrayDataSetTuple byPath.AromaUnitCallSet byPath.AromaUnitGenotypeCallSet calcMargins calcMargins.matrix calculateAverageColumnAcrossFiles calculateAverageColumnAcrossFiles.GenericTabularFileSet calculateChromosomeStatistics calculateChromosomeStatistics.CopyNumberChromosomalModel calculateRatios calculateRatios.CopyNumberChromosomalModel clearCache.AromaTabularBinaryFile clearCache.AromaTransform clearCache.AromaUnitChromosomeTabularBinaryFile clearCache.AromaUnitTabularBinaryFile clearCache.ChromosomalModel clearCache.CopyNumberChromosomalModel clearCache.TextUnitNamesFile cnRange cnRange.RawCopyNumbers colGaussianSmoothing colGaussianSmoothing.matrix colMeans colMeans.AromaTabularBinaryFile colMeans.default colMedians.AromaTabularBinaryFile colorize colorize.Image colStats colStats.AromaTabularBinaryFile colSums colSums.AromaTabularBinaryFile colSums.default convertTable convertTable.default CopyNumberDataFile CopyNumberDataSet CopyNumberDataSetTuple CopyNumberOutliers CopyNumberRegions countBases countBases.AromaCellSequenceFile countBasesInternal countBasesInternal.AromaCellSequenceFile dimnames<-.AromaTabularBinaryFile display display.ChromosomeExplorer display.Image divideBy divideBy.RawGenomicSignals drawCnRegions drawCnRegions.DNAcopy drawCnRegions.HaarSeg drawCnRegions.profileCGH drawCytoband drawCytoband.ChromosomalModel drawCytoband.profileCGH drawCytoband2 drawCytoband2.default drawExtraAnnotations drawExtraAnnotations.default drawExtraAnnotations.profileCGH drawLevels drawLevels.CopyNumberOutliers drawLevels.CopyNumberRegions estimateSds estimateStandardDeviation exportFracBDiffSet exportFracBDiffSet.AromaUnitFracBCnBinarySet exportTotalCnRatioSet exportTotalCnRatioSet.AromaUnitTotalCnBinarySet extractByChromosome extractByChromosome.AromaUnitChromosomeTabularBinaryFile extractCallArray extractCallArray.AromaUnitCallFile extractCallArray.AromaUnitCallSet extractCalls extractCalls.AromaUnitCallFile extractCalls.AromaUnitCallSet extractCNRs extractCNRs.default extractCopyNumberOutliers extractCopyNumberOutliers.DNAcopy extractCopyNumberOutliers.profileCGH extractCopyNumberRegions extractCopyNumberRegions.default extractCopyNumberRegions.DNAcopy extractCopyNumberRegions.HaarSeg extractCopyNumberRegions.profileCGH extractDataForSegmentation extractDataForSegmentation.RawGenomicSignals extractGenotypeMatrix extractGenotypeMatrix.AromaUnitCallSet extractGenotypeMatrix.AromaUnitGenotypeCallFile extractGenotypes extractGenotypes.AromaUnitGenotypeCallFile extractGenotypes.AromaUnitGenotypeCallSet extractIGV extractIGV.CopyNumberRegions extractMatrix.AromaUnitCallFile extractMatrix.AromaUnitSignalBinaryFile extractMergedRawCopyNumbers extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList extractOld extractOld.AromaMicroarrayDataSetTuple extractRawAlleleBFractions extractRawAlleleBFractions.AromaUnitFracBCnBinaryFile extractRawAlleleBFractions.default extractRawCNs extractRawCNs.default extractRawCopyNumbers extractRawCopyNumbers.AromaUnitTotalCnBinaryFile extractRawCopyNumbers.AromaUnitTotalCnBinaryFileList extractRawCopyNumbers.default extractRawCopyNumbers.DNAcopy extractRawCopyNumbers.HaarSeg extractRawCopyNumbers.profileCGH extractRawCopyNumbers.RawCopyNumbers extractRawCopyNumbers.RawSequenceReads extractRawGenomicSignals extractRawGenomicSignals.AromaUnitSignalBinaryFile extractRawGenomicSignals.AromaUnitTotalCnBinaryFileList extractRawGenomicSignals.default extractRawMirroredAlleleBFractions extractRawMirroredAlleleBFractions.default extractRawMirroredAlleleBFractions.RawAlleleBFractions extractRegion extractRegion.RawGenomicSignals extractSubset extractSubset.RawGenomicSignals extractSubsetByState extractSubsetByState.SegmentedGenomicSignalsInterface findByChipType findByChipType.AromaMicroarrayTabularBinaryFile findByChipType.TextUnitNamesFile findByName.AromaUnitCallSet findByName.AromaUnitSignalBinarySet findPngDevice findPngDevice.default findSAFs findSAFs.SampleAnnotationSet findUnitNamesFile findUnitNamesFile.AromaPlatform findUnitsTodo findUnitsTodo.AromaUnitCallFile findUnitsTodo.AromaUnitCallSet findUnitTypesFile findUnitTypesFile.AromaPlatform fit fit.ChromosomalModel fit2d fit2d.matrix fitGenotypeCone fitGenotypeConeByExpectile fitGenotypeConeByExpectile.matrix fitGenotypeConeBySfit fitMultiDimensionalCone fitProbePositionEffects fitProbePositionEffects.numeric fitSplineBlockPolish fitSplineBlockPolish.matrix fitWHLAPLM fitWHLAPLM.matrix fitWHRCModel fitWHRCModel.matrix fitWLAPLM fitWLAPLM.matrix fitWRCModel fitWRCModel.matrix fitWRMA fitWRMA.matrix fixSearchPath fixSearchPath.AromaCore fixSearchPath.AromaPackage fixSearchPathInternal fixSearchPathInternal.AromaPackage fromFile.AromaUnitSignalBinaryFile fromPath fromPath.SampleAnnotationFile fromPath.SampleAnnotationSet gaussianSmoothing gaussianSmoothing.matrix gaussianSmoothing.numeric gaussianSmoothing.RawGenomicSignals gaussKernel getAlias.ChromosomalModel getAM getAM.AromaUnitTotalCnBinaryFile getAromaPlatform getAromaPlatform.AromaPlatformInterface getAromaUflFile getAromaUflFile.UnitAnnotationDataFile getAromaUgpFile getAromaUgpFile.AromaPlatform getAromaUgpFile.AromaUnitSignalBinaryFile getAromaUgpFile.AromaUnitSignalBinarySet getAromaUgpFile.UnitAnnotationDataFile getArrays getArrays.AromaMicroarrayDataSetTuple getArrays.ChromosomalModel getArrays.Explorer getArraysOfInput getArraysOfInput.ChromosomeExplorer getArraysOfInput.Explorer getArrayTuple getArrayTuple.AromaMicroarrayDataSetTuple getAsteriskTags.AromaMicroarrayDataSetTuple getAsteriskTags.AromaTransform getAsteriskTags.ChromosomalModel getAsteriskTags.CopyNumberSegmentationModel getAsteriskTags.Explorer getAsteriskTags.HaarSegModel getAsteriskTags.RawCopyNumberModel getAttributeXY getAttributeXY.AromaMicroarrayDataFile getAverageFile getAverageFile.AromaMicroarrayDataSet getAverageFile.AromaUnitTotalCnBinarySet getBytesPerColumn getBytesPerColumn.AromaTabularBinaryFile getChipEffectFiles getChipEffectFiles.ChromosomalModel getChipType getChipType.AromaMicroarrayDataFile getChipType.AromaMicroarrayDataSet getChipType.AromaMicroarrayTabularBinaryFile getChipType.AromaUnitSignalBinaryFile getChipType.AromaUnitSignalBinarySet getChipType.AromaUnitTypesFile getChipType.TextUnitNamesFile getChipType.UnitAnnotationDataFile getChipTypes getChipTypes.AromaMicroarrayDataSetTuple getChipTypes.ChromosomalModel getChromosome getChromosome.Arguments getChromosome.RawGenomicSignals getChromosomes getChromosomes.Arguments getChromosomes.AromaUnitChromosomeTabularBinaryFile getCn getCn.RawCopyNumbers getCNs getCNs.RawCopyNumbers getColClasses getColClasses.AromaTabularBinaryFile getColumnNames.AromaCellPositionFile getColumnNames.AromaCellSequenceFile getColumnNames.AromaTabularBinaryFile getColumnNames.AromaUflFile getColumnNames.AromaUgpFile getColumnNames.AromaUnitChromosomeTabularBinaryFile getCommonListElements getDataFileMatrix getDataFileMatrix.CopyNumberChromosomalModel getDeviceResolution getDeviceResolution.default getEffects getEffects.ProbePositionEffects getExpectedOutputFiles getExpectedOutputFiles.AromaTransform getExpectedOutputFullnames getExpectedOutputFullnames.AromaTransform getExtensionPattern.AromaCellPositionFile getExtensionPattern.AromaCellSequenceFile getExtensionPattern.AromaUflFile getExtensionPattern.AromaUgpFile getExtensionPattern.AromaUnitSignalBinaryFile getExtensionPattern.SampleAnnotationFile getExtensionPattern.TextUnitNamesFile getFilenameExtension.AromaCellPositionFile getFilenameExtension.AromaCellSequenceFile getFilenameExtension.AromaMicroarrayTabularBinaryFile getFilenameExtension.AromaUflFile getFilenameExtension.AromaUgpFile getFilenameExtension.AromaUnitChromosomeTabularBinaryFile getFilenameExtension.AromaUnitSignalBinaryFile getFilenameExtension.TextUnitNamesFile getFitFunction getFitFunction.CbsModel getFitFunction.CopyNumberSegmentationModel getFitFunction.GladModel getFitFunction.HaarSegModel getFullName.ChromosomalModel getFullName.Explorer getFullNames.AromaMicroarrayDataSetTuple getFullNames.ChromosomalModel getFullNames.ChromosomeExplorer getFullNames.CopyNumberSegmentationModel getGenome getGenome.ChromosomalModel getGenomeData getGenomeData.ChromosomalModel getGenomeFile getGenomeFile.ChromosomalModel getGenomeVersion getGenomeVersion.AromaUnitChromosomeTabularBinaryFile getHeaderParameters getHeaderParameters.TextUnitNamesFile getImage getImage.matrix getIncludePath getIncludePath.Explorer getInputDataSet getLabel.AromaMicroarrayDataFile getListOfAromaUgpFiles getListOfAromaUgpFiles.ChromosomalModel getListOfChipEffectSets getListOfChipEffectSets.ChromosomalModel getListOfUnitNamesFiles getListOfUnitNamesFiles.AromaUnitTotalCnBinarySetTuple getListOfUnitNamesFiles.ChromosomalModel getListOfUnitTypesFiles getListOfUnitTypesFiles.ChromosomalModel getLociFields getLociFields.RawGenomicSignals getLocusFields getLocusFields.RawGenomicSignals getLog2Ratios getLog2Ratios.CopyNumberSegmentationModel getMainPath getMainPath.Explorer getMaxLengthRepeats getMaxLengthRepeats.AromaCellSequenceFile getModel getName.AromaPlatform getName.ChromosomalModel getName.RawGenomicSignals getNameOfInput getNameOfInput.ChromosomeExplorer getNameOfInput.Explorer getNames.ChromosomeExplorer getNames.CopyNumberChromosomalModel getNumberOfFilesAveraged getNumberOfFilesAveraged.AromaUnitTotalCnBinaryFile getNumberOfFilesAveraged.CopyNumberDataFile getOutputDataSet getOutputDataSet0 getOutputDataSet0.AromaTransform getOutputFiles getOutputFiles.AromaTransform getPairedNames getPairedNames.CopyNumberChromosomalModel getParallelSafe getParallelSafe.Explorer getParameters.AromaTransform getParametersAsString getParametersAsString.AromaTransform getParentPath getParentPath.ChromosomalModel getPath.ChromosomalModel getPath.ChromosomeExplorer getPath.Explorer getPatterns getPatterns.SampleAnnotationFile getPhysicalPositions getPhysicalPositions.RawCopyNumbers getPlatform getPlatform.AromaMicroarrayDataFile getPlatform.AromaMicroarrayDataSet getPlatform.AromaMicroarrayTabularBinaryFile getPlatform.AromaPlatformInterface getPlatform.AromaUnitSignalBinaryFile getPlatform.AromaUnitSignalBinarySet getPlatform.AromaUnitTypesFile getPlatform.TextUnitNamesFile getPlatform.UnitAnnotationDataFile getPloidy getPloidy.AromaMicroarrayDataFile getPositions getPositions.AromaUgpFile getPositions.RawGenomicSignals getProbeLength getProbeLength.AromaCellSequenceFile getProbePositionEffectDesignMatrix getProbePositionEffectDesignMatrix.character getProbePositionEffectDesignMatrix.raw getRam getRam.AromaSettings getRawCnData getRawCnData.CopyNumberChromosomalModel getReferenceSetTuple getReferenceSetTuple.CopyNumberChromosomalModel getRefSetTuple getRefSetTuple.CopyNumberChromosomalModel getRegions getRegions.CopyNumberSegmentationModel getReportPath getReportPath.ChromosomalModel getReportPathPattern getReportPathPattern.Explorer getRootPath getRootPath.AromaTransform getRootPath.ChromosomalModel getRootPath.Explorer getSampleLabels getSampleLabels.ChromosomeExplorer getSampleLayerName getSampleLayerName.Explorer getSampleLayerPrefix getSampleLayerPrefix.Explorer getSets.AromaMicroarrayDataSetTuple getSets.ChromosomalModel getSetTag getSetTag.ChromosomalModel getSetTag.RawCopyNumberModel getSetTuple getSetTuple.ChromosomalModel getSigma getSigma.RawGenomicSignals getSignals getSignals.RawGenomicSignals getSnpNucleotides getSnpNucleotides.AromaCellSequenceFile getSnpPositions getSnpPositions.AromaCellSequenceFile getSnpShifts getSnpShifts.AromaCellSequenceFile getStateColorMap getStateColorMap.SegmentedGenomicSignalsInterface getStateColors getStateColors.SegmentedGenomicSignalsInterface getStates getStates.SegmentedGenomicSignalsInterface getSubname getSubname.Explorer getTableOfArrays getTableOfArrays.AromaMicroarrayDataSetTuple getTableOfArrays.ChromosomalModel getTags.AromaMicroarrayDataSetTuple getTags.ChromosomalModel getTags.CopyNumberSegmentationModel getTagsOfInput getTagsOfInput.ChromosomeExplorer getTagsOfInput.Explorer getTemplatePath getTemplatePath.Explorer getUniqueStates getUniqueStates.SegmentedGenomicSignalsInterface getUnitAnnotationDataFile getUnitAnnotationDataFile.AromaPlatformInterface getUnitNames getUnitNames.TextUnitNamesFile getUnitNames.UnitNamesFile getUnitNamesFile getUnitNamesFile.AromaPlatform getUnitNamesFile.AromaPlatformInterface getUnitNamesFile.AromaUnitTotalCnBinarySet getUnitsAt getUnitsAt.AromaUgpFile getUnitsOnChromosome getUnitsOnChromosome.AromaUgpFile getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile getUnitsOnChromosomes getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile getUnitTypes getUnitTypes.AromaUnitTypesFile getUnitTypes.UnitTypesFile getUnitTypesFile getUnitTypesFile.AromaPlatform getUnitTypesFile.AromaPlatformInterface getVerbose.AromaSettings getWeights getWeights.RawGenomicSignals getXAM getXAM.AromaMicroarrayDataFile getXAM.AromaUnitTotalCnBinaryFile getXScale getXScale.RawGenomicSignals getXY getXY.RawGenomicSignals getYScale getYScale.RawGenomicSignals getZooms getZooms.ChromosomeExplorer groupBySnpNucleotides groupBySnpNucleotides.AromaCellSequenceFile hasAlleleBFractions hasAlleleBFractions.AromaUnitTotalCnBinaryFile hasAlleleBFractions.CopyNumberDataFile hasAlleleBFractions.CopyNumberDataSet hasAlleleBFractions.CopyNumberDataSetTuple hasAttributeXY hasAttributeXY.AromaMicroarrayDataFile hasStrandiness hasStrandiness.AromaUnitTotalCnBinaryFile hasStrandiness.CopyNumberDataFile hasStrandiness.CopyNumberDataSet hasStrandiness.CopyNumberDataSetTuple hasWeights hasWeights.RawGenomicSignals importFrom importFrom.AromaTabularBinaryFile importFromGenericTabularFile importFromGenericTabularFile.AromaUflFile importFromGenericTabularFile.AromaUgpFile importFromTable importFromTable.FileMatrix importFromUnitTypesFile importFromUnitTypesFile.AromaUnitTypesFile indexOf.AromaMicroarrayDataSetTuple indexOf.ChromosomalModel indexOf.ChromosomeExplorer indexOfColumn indexOfColumn.AromaUnitChromosomeTabularBinaryFile indexOfUnits indexOfUnits.AromaUnitTabularBinaryFile interleave interleave.Image isAverageFile isAverageFile.AromaMicroarrayDataFile isAverageFile.AromaUnitSignalBinaryFile isHeterozygote isHeterozygote.AromaUnitGenotypeCallFile isHeterozygous isHeterozygous.AromaUnitGenotypeCallFile isHomozygote isHomozygote.AromaUnitGenotypeCallFile isHomozygous isHomozygous.AromaUnitGenotypeCallFile isMissing isMissing.AromaCellPositionFile isMissing.AromaCellSequenceFile isPaired isPaired.CopyNumberChromosomalModel kernelSmoothing.RawGenomicSignals kernelSmoothingByState kernelSmoothingByState.SegmentedGenomicSignalsInterface lapply.AromaTabularBinaryFile lapplyInChunks lapplyInChunks.numeric library lines.CopyNumberOutliers lines.CopyNumberRegions lines.RawGenomicSignals listToXml listToXml.list locallyUnique locallyUnique.default log2abs log2center log2neg log2pos matchPatterns matchPatterns.SampleAnnotationFile matrixBlockPolish mergeBoxplotStats multiplyBy multiplyBy.RawGenomicSignals nbrOfArrays nbrOfArrays.AromaMicroarrayDataSet nbrOfArrays.AromaMicroarrayDataSetTuple nbrOfArrays.AromaUnitTotalCnBinarySet nbrOfCells nbrOfCells.AromaCellTabularBinaryFile nbrOfChipTypes nbrOfColumns.AromaTabularBinaryFile nbrOfEnzymes nbrOfEnzymes.AromaUflFile nbrOfLoci nbrOfLoci.RawGenomicSignals nbrOfReads nbrOfReads.RawSequenceReads nbrOfRegions nbrOfRegions.CopyNumberOutliers nbrOfRegions.CopyNumberRegions nbrOfRows.AromaTabularBinaryFile nbrOfUnits nbrOfUnits.AromaUnitSignalBinaryFile nbrOfUnits.AromaUnitTabularBinaryFile nbrOfUnits.TextUnitNamesFile nbrOfUnits.UnitAnnotationDataFile nbrOfUnits.UnitNamesFile nbrOfUnits.UnitTypesFile newPlot newPlot.CopyNumberChromosomalModel norm2d norm2d.matrix normalizeGenotypeCone normalizeGenotypeCone.matrix onFitAddGenotypeCalls onFitAddGenotypeCalls.default onFitAddGenotypeCalls.GladModel patch patch.AromaPackage plot.BinnedScatter plot.CopyNumberSegmentationModel plot.ProbePositionEffects plot.profileCGH plot.RawAlleleBFractions plot.RawCopyNumbers plot.RawGenomicSignals plot.RawMirroredAlleleBFractions plot.RawSequenceReads plot.SegmentedGenomicSignalsInterface plotAxesLayers plotAxesLayers.CopyNumberChromosomalModel plotChromosomesLayers plotChromosomesLayers.CopyNumberChromosomalModel plotCopyNumberRegionLayers plotCopyNumberRegionLayers.CopyNumberSegmentationModel plotCytobandLayers plotCytobandLayers.CopyNumberChromosomalModel plotFitLayers plotFitLayers.CopyNumberChromosomalModel plotGridHorizontalLayers plotGridHorizontalLayers.CopyNumberChromosomalModel plotProfile2 plotProfile2.profileCGH plotRawCNs plotRawCNs.profileCGH plotRawCopyNumbers plotRawCopyNumbers.CopyNumberChromosomalModel plotSampleLayers plotSampleLayers.CopyNumberChromosomalModel points.BinnedScatter points.RawGenomicSignals points.SegmentedGenomicSignalsInterface pointsRawCNs pointsRawCNs.default pointsRawCNs.profileCGH pointsSequence pointsSequence.ProbePositionEffects predict.ProbePositionEffects process readColumns.AromaTabularBinaryFile readData readData.SampleAnnotationFile readDataFrame.AromaTabularBinaryFile readDataFrame.AromaUflFile readDataFrame.AromaUnitChromosomeTabularBinaryFile readDataFrame.AromaUnitSignalBinaryFile readDataFrame.SampleAnnotationFile readFooter readHeader readHeader.AromaTabularBinaryFile readNeighborSequenceMatrix readNeighborSequenceMatrix.AromaCellSequenceFile readPairSequenceMatrix readPairSequenceMatrix.AromaCellSequenceFile readPositions readPositions.AromaCellPositionFile readRawFooter readRawFooter.AromaTabularBinaryFile readSequenceMatrix readSequenceMatrix.AromaCellSequenceFile readSequences readSequences.AromaCellSequenceFile readTargetStrands readTargetStrands.AromaCellSequenceFile remap remap.default reorder.BinnedScatter require rescale rescale.Image rgbTransform rgbTransform.Image SampleAnnotationFile SampleAnnotationSet segmentByCBS segmentByGLAD segmentByHaarSeg setAlias.ChromosomalModel setArrays setAttributesBy.AromaMicroarrayDataSet setAttributesBySampleAnnotationFile setAttributesBySampleAnnotationFile.AromaMicroarrayDataSet setAttributesBySampleAnnotationSet setAttributesBySampleAnnotationSet.AromaMicroarrayDataSet setAttributesByTags.AromaMicroarrayDataFile setAttributesByTags.AromaTabularBinaryFile setAttributeXY setAttributeXY.AromaMicroarrayDataFile setCytoband setCytoband.ChromosomeExplorer setGenome setGenome.ChromosomalModel setLabel.AromaMicroarrayDataFile setLocusFields setLocusFields.RawGenomicSignals setName.RawGenomicSignals setParallelSafe setParallelSafe.Explorer setRam setRam.AromaSettings setReportPathPattern setReportPathPattern.Explorer setSigma setSigma.RawGenomicSignals setStateColorMap setStateColorMap.SegmentedGenomicSignalsInterface setStates setStates.SegmentedGenomicSignalsInterface setSubname setSubname.Explorer setTags.AromaTransform setup setup.ChromosomeExplorer setup.Explorer setVerbose setVerbose.AromaSettings setWeights setWeights.RawGenomicSignals setXScale setXScale.RawGenomicSignals setYScale setYScale.RawGenomicSignals setZooms setZooms.ChromosomeExplorer shakyText shakyText.default signalRange signalRange.RawGenomicSignals smoothWRMA smoothWRMA.matrix smoothWSA smoothWSA.matrix sort.RawGenomicSignals splitByReportPathPattern splitByReportPathPattern.Explorer splitInChunks splitInChunks.numeric sqrtabs sqrtcenter sqrtneg sqrtpos stext stext.default stextChipType stextChipType.character stextLabel stextLabel.AromaMicroarrayDataFile stextLabels stextLabels.AromaMicroarrayDataFile stextSize stextSize.AromaMicroarrayDataFile stringTree stringTree.character subsample subsample.BinnedScatter subset.AromaTabularBinaryFile subset.BinnedScatter subtractBy subtractBy.RawGenomicSignals summary.AromaTabularBinaryFile summary.RawGenomicSignals summaryOfUnits summaryOfUnits.AromaUflFile text.ProbePositionEffects textSequence textSequence.ProbePositionEffects TextUnitNamesFile updateData updateData.AromaTabularBinaryFile updateDataColumn updateDataColumn.AromaTabularBinaryFile updateGenotypes updateGenotypes.AromaUnitGenotypeCallFile updatePositions updatePositions.AromaCellPositionFile updateSamplesFile updateSequenceMatrix updateSequenceMatrix.AromaCellSequenceFile updateSequences updateSequences.AromaCellSequenceFile updateTargetStrands updateTargetStrands.AromaCellSequenceFile validate.AromaMicroarrayDataSet validate.AromaUnitSignalBinarySet weightedMad weightedMean whatDataType whatDataType.default writeAxesLayers writeAxesLayers.ChromosomeExplorer writeCopyNumberRegionLayers writeCopyNumberRegionLayers.ChromosomeExplorer writeCytobandLayers writeCytobandLayers.ChromosomeExplorer writeFooter writeGraphs writeGraphs.ChromosomeExplorer writeGridHorizontalLayers writeGridHorizontalLayers.ChromosomeExplorer writeRawCopyNumberLayers writeRawCopyNumberLayers.ChromosomeExplorer writeRawFooter writeRawFooter.AromaTabularBinaryFile writeRegions writeRegions.ChromosomeExplorer writeRegions.CopyNumberSegmentationModel writeRegions.GladModel xMax xMax.RawGenomicSignals xMin xMin.RawGenomicSignals xmlToList xmlToList.character xRange xRange.RawGenomicSignals xSeq xSeq.RawGenomicSignals yellow.colors yMax yMax.RawGenomicSignals yMin yMin.RawGenomicSignals yRange yRange.RawGenomicSignals getDefaultFullName.AromaMicroarrayDataSet getDefaultFullName.AromaTabularBinarySet drawCnRegions.MPCBS extractCopyNumberRegions.MPCBS segmentByMPCBS segmentByMPCBS.RawGenomicSignals
Keywords: documentation internal
Description: Non-documented objects
URL: ../../../library/aroma.core/html/Non-documented_objects.html

Entry: RawAlleleBFractions
Aliases: RawAlleleBFractions
Keywords: classes
Description: The RawAlleleBFractions class
URL: ../../../library/aroma.core/html/RawAlleleBFractions.html

Entry: RawCopyNumberModel
Aliases: RawCopyNumberModel
Keywords: classes
Description: The RawCopyNumberModel class
URL: ../../../library/aroma.core/html/RawCopyNumberModel.html

Entry: RawCopyNumbers
Aliases: RawCopyNumbers
Keywords: classes
Description: The RawCopyNumbers class
URL: ../../../library/aroma.core/html/RawCopyNumbers.html

Entry: RawGenomicSignals
Aliases: RawGenomicSignals
Keywords: classes
Description: The RawGenomicSignals class
URL: ../../../library/aroma.core/html/RawGenomicSignals.html

Entry: RawMirroredAlleleBFractions
Aliases: RawMirroredAlleleBFractions
Keywords: classes
Description: The RawMirroredAlleleBFractions class
URL: ../../../library/aroma.core/html/RawMirroredAlleleBFractions.html

Entry: RawSequenceReads
Aliases: RawSequenceReads
Keywords: classes
Description: The RawSequenceReads class
URL: ../../../library/aroma.core/html/RawSequenceReads.html

Entry: SegmentedAlleleBFractions
Aliases: SegmentedAlleleBFractions
Keywords: classes
Description: The SegmentedAlleleBFractions class
URL: ../../../library/aroma.core/html/SegmentedAlleleBFractions.html

Entry: SegmentedCopyNumbers
Aliases: SegmentedCopyNumbers
Keywords: classes
Description: The SegmentedCopyNumbers class
URL: ../../../library/aroma.core/html/SegmentedCopyNumbers.html

Entry: SegmentedGenomicSignalsInterface
Aliases: SegmentedGenomicSignalsInterface
Keywords: classes
Description: The SegmentedGenomicSignalsInterface class interface
URL: ../../../library/aroma.core/html/SegmentedGenomicSignalsInterface.html

Entry: UnitAnnotationDataFile
Aliases: UnitAnnotationDataFile
Keywords: classes
Description: The UnitAnnotationDataFile interface class
URL: ../../../library/aroma.core/html/UnitAnnotationDataFile.html

Entry: UnitNamesFile
Aliases: UnitNamesFile
Keywords: classes
Description: The UnitNamesFile interface class
URL: ../../../library/aroma.core/html/UnitNamesFile.html

Entry: UnitTypesFile
Aliases: UnitTypesFile
Keywords: classes
Description: The UnitTypesFile interface class
URL: ../../../library/aroma.core/html/UnitTypesFile.html

Entry: allocate.AromaTabularBinaryFile
Aliases: allocate.AromaTabularBinaryFile AromaTabularBinaryFile.allocate allocate.AromaTabularBinaryFile allocate,AromaTabularBinaryFile-method
Keywords: internal methods IO
Description: Creates an AromaTabularBinaryFile
URL: ../../../library/aroma.core/html/allocate.AromaTabularBinaryFile.html

Entry: aroma.core-package
Aliases: aroma.core-package aroma.core
Keywords: package
Description: Package aroma.core
URL: ../../../library/aroma.core/html/aroma.core-package.html

Entry: as.GrayscaleImage.matrix
Aliases: as.GrayscaleImage.matrix as.GrayscaleImage.matrix matrix.as.TrueColorsImage as.TrueColorsImage.matrix as.TrueColorsImage,matrix-method
Keywords: methods IO
Description: Creates a Grayscale (TrueColor) Image from a matrix file
URL: ../../../library/aroma.core/html/as.GrayscaleImage.matrix.html

Entry: colBinnedSmoothing.matrix
Aliases: colBinnedSmoothing.matrix colBinnedSmoothing.matrix colBinnedSmoothing binnedSmoothing binnedSmoothing.numeric
Keywords: methods array iteration robust univar
Description: Binned smoothing of a matrix column by column
URL: ../../../library/aroma.core/html/colBinnedSmoothing.matrix.html

Entry: colKernelSmoothing.matrix
Aliases: colKernelSmoothing.matrix colKernelSmoothing.matrix colKernelSmoothing kernelSmoothing kernelSmoothing.numeric
Keywords: methods array iteration robust univar
Description: Kernel smoothing of a matrix column by column
URL: ../../../library/aroma.core/html/colKernelSmoothing.matrix.html

Entry: display.Explorer
Aliases: display.Explorer Explorer.display display.Explorer display,Explorer-method
Keywords: internal methods
Description: Displays the explorer in the default browser
URL: ../../../library/aroma.core/html/display.Explorer.html

Entry: downloadPackagePatch
Aliases: downloadPackagePatch.default downloadPackagePatch
Keywords: internal
Description: Download a package patch
URL: ../../../library/aroma.core/html/downloadPackagePatch.html

Entry: estimateSds.CopyNumberChromosomalModel
Aliases: estimateSds.CopyNumberChromosomalModel CopyNumberChromosomalModel.estimateSds estimateSds.CopyNumberChromosomalModel estimateSds,CopyNumberChromosomalModel-method
Keywords: internal methods
Description: Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
URL: ../../../library/aroma.core/html/estimateSds.CopyNumberChromosomalModel.html

Entry: estimateStandardDeviation.RawGenomicSignals
Aliases: estimateStandardDeviation.RawGenomicSignals RawGenomicSignals.estimateStandardDeviation estimateStandardDeviation.RawGenomicSignals estimateStandardDeviation,RawGenomicSignals-method
Keywords: internal methods IO programming
Description: Estimates the standard deviation of the raw Ys
URL: ../../../library/aroma.core/html/estimateStandardDeviation.RawGenomicSignals.html

Entry: extractRawCopyNumbers.CopyNumberChromosomalModel
Aliases: extractRawCopyNumbers.CopyNumberChromosomalModel CopyNumberChromosomalModel.extractRawCopyNumbers extractRawCopyNumbers.CopyNumberChromosomalModel extractRawCopyNumbers,CopyNumberChromosomalModel-method
Keywords: internal methods
Description: Extracts relative copy numbers
URL: ../../../library/aroma.core/html/extractRawCopyNumbers.CopyNumberChromosomalModel.html

Entry: findAnnotationData
Aliases: findAnnotationData.default findAnnotationData
Keywords: internal
Description: Locates an annotation data file
URL: ../../../library/aroma.core/html/findAnnotationData.html

Entry: findAnnotationDataByChipType
Aliases: findAnnotationDataByChipType.default findAnnotationDataByChipType
Keywords: internal
Description: Locates an annotation data file by its chip type
URL: ../../../library/aroma.core/html/findAnnotationDataByChipType.html

Entry: fit.CopyNumberChromosomalModel
Aliases: fit.CopyNumberChromosomalModel CopyNumberChromosomalModel.fit fit.CopyNumberChromosomalModel fit,CopyNumberChromosomalModel-method
Keywords: internal methods
Description: Fits the model
URL: ../../../library/aroma.core/html/fit.CopyNumberChromosomalModel.html

Entry: fit.CopyNumberSegmentationModel
Aliases: fit.CopyNumberSegmentationModel CopyNumberSegmentationModel.fit fit.CopyNumberSegmentationModel fit,CopyNumberSegmentationModel-method
Keywords: internal methods
Description: Fits the model
URL: ../../../library/aroma.core/html/fit.CopyNumberSegmentationModel.html

Entry: fitGenotypeCone.matrix
Aliases: fitGenotypeCone.matrix fitGenotypeCone.matrix
Keywords: methods internal
Description: Fits an affine transformation to allele A and allele B data
URL: ../../../library/aroma.core/html/fitGenotypeCone.matrix.html

Entry: fitGenotypeConeBySfit.matrix
Aliases: fitGenotypeConeBySfit.matrix fitGenotypeConeBySfit.matrix
Keywords: methods internal
Description: Fits an affine transformation to allele A and allele B data
URL: ../../../library/aroma.core/html/fitGenotypeConeBySfit.matrix.html

Entry: fitMultiDimensionalCone.matrix
Aliases: fitMultiDimensionalCone.matrix fitMultiDimensionalCone.matrix
Keywords: methods internal
Description: Fits an affine transformation to multi-dimensional data
URL: ../../../library/aroma.core/html/fitMultiDimensionalCone.matrix.html

Entry: getAlias.Explorer
Aliases: getAlias.Explorer Explorer.getAlias getAlias.Explorer getAlias,Explorer-method
Keywords: internal methods
Description: Gets the alias of the output set
URL: ../../../library/aroma.core/html/getAlias.Explorer.html

Entry: getChipType.ChromosomalModel
Aliases: getChipType.ChromosomalModel ChromosomalModel.getChipType getChipType.ChromosomalModel getChipType,ChromosomalModel-method
Keywords: internal methods
Description: Gets a label for all chip types merged
URL: ../../../library/aroma.core/html/getChipType.ChromosomalModel.html

Entry: getChromosomes.ChromosomalModel
Aliases: getChromosomes.ChromosomalModel ChromosomalModel.getChromosomes getChromosomes.ChromosomalModel getChromosomes,ChromosomalModel-method
Keywords: internal methods
Description: Gets the chromosomes available
URL: ../../../library/aroma.core/html/getChromosomes.ChromosomalModel.html

Entry: getChromosomes.ChromosomeExplorer
Aliases: getChromosomes.ChromosomeExplorer ChromosomeExplorer.getChromosomes getChromosomes.ChromosomeExplorer getChromosomes,ChromosomeExplorer-method
Keywords: internal methods
Description: Gets the chromosomes available
URL: ../../../library/aroma.core/html/getChromosomes.ChromosomeExplorer.html

Entry: getFullName.AromaTransform
Aliases: getFullName.AromaTransform AromaTransform.getFullName getFullName.AromaTransform getFullName,AromaTransform-method
Keywords: internal methods
Description: Gets the full name of the output data set
URL: ../../../library/aroma.core/html/getFullName.AromaTransform.html

Entry: getInputDataSet.AromaTransform
Aliases: getInputDataSet.AromaTransform AromaTransform.getInputDataSet getInputDataSet.AromaTransform getInputDataSet,AromaTransform-method
Keywords: internal methods
Description: Gets the input data set
URL: ../../../library/aroma.core/html/getInputDataSet.AromaTransform.html

Entry: getModel.ChromosomeExplorer
Aliases: getModel.ChromosomeExplorer ChromosomeExplorer.getModel getModel.ChromosomeExplorer getModel,ChromosomeExplorer-method
Keywords: internal methods
Description: Gets the model
URL: ../../../library/aroma.core/html/getModel.ChromosomeExplorer.html

Entry: getName.AromaTransform
Aliases: getName.AromaTransform AromaTransform.getName getName.AromaTransform getName,AromaTransform-method
Keywords: internal methods
Description: Gets the name of the output data set
URL: ../../../library/aroma.core/html/getName.AromaTransform.html

Entry: getName.Explorer
Aliases: getName.Explorer Explorer.getName getName.Explorer getName,Explorer-method
Keywords: internal methods
Description: Gets the name of the explorer
URL: ../../../library/aroma.core/html/getName.Explorer.html

Entry: getNames.ChromosomalModel
Aliases: getNames.ChromosomalModel ChromosomalModel.getNames getNames.ChromosomalModel getNames,ChromosomalModel-method
Keywords: internal methods
Description: Gets the names of the arrays
URL: ../../../library/aroma.core/html/getNames.ChromosomalModel.html

Entry: getNames.Explorer
Aliases: getNames.Explorer Explorer.getNames getNames.Explorer getNames,Explorer-method
Keywords: internal methods
Description: Gets the names of the input samples
URL: ../../../library/aroma.core/html/getNames.Explorer.html

Entry: getOutputDataSet.AromaTransform
Aliases: getOutputDataSet.AromaTransform AromaTransform.getOutputDataSet getOutputDataSet.AromaTransform getOutputDataSet,AromaTransform-method
Keywords: internal methods
Description: Gets the transformed data set
URL: ../../../library/aroma.core/html/getOutputDataSet.AromaTransform.html

Entry: getPath.AromaTransform
Aliases: getPath.AromaTransform AromaTransform.getPath getPath.AromaTransform getPath,AromaTransform-method
Keywords: internal methods
Description: Gets the path of the output data set
URL: ../../../library/aroma.core/html/getPath.AromaTransform.html

Entry: getTags.AromaTransform
Aliases: getTags.AromaTransform AromaTransform.getTags getTags.AromaTransform getTags,AromaTransform-method
Keywords: internal methods
Description: Gets the tags of the output data set
URL: ../../../library/aroma.core/html/getTags.AromaTransform.html

Entry: getTags.Explorer
Aliases: getTags.Explorer Explorer.getTags getTags.Explorer getTags,Explorer-method
Keywords: internal methods
Description: Gets the tags of the explorer
URL: ../../../library/aroma.core/html/getTags.Explorer.html

Entry: indexOf.UnitNamesFile
Aliases: indexOf.UnitNamesFile UnitNamesFile.indexOf indexOf.UnitNamesFile indexOf,UnitNamesFile-method
Keywords: internal methods IO
Description: Gets the indices of units by their names
URL: ../../../library/aroma.core/html/indexOf.UnitNamesFile.html

Entry: isDone.AromaTransform
Aliases: isDone.AromaTransform AromaTransform.isDone isDone.AromaTransform isDone,AromaTransform-method
Keywords: internal methods
Description: Checks if the data set is processed or not
URL: ../../../library/aroma.core/html/isDone.AromaTransform.html

Entry: matrixBlockPolish.matrix
Aliases: matrixBlockPolish.matrix matrixBlockPolish.matrix
Keywords: methods internal
Description: Applies a polishing function to blocks of rows and columns repeatedly
URL: ../../../library/aroma.core/html/matrixBlockPolish.matrix.html

Entry: mergeBoxplotStats.list
Aliases: mergeBoxplotStats.list mergeBoxplotStats.list
Keywords: methods internal
Description: Merges a list of boxplot.stats() elements
URL: ../../../library/aroma.core/html/mergeBoxplotStats.list.html

Entry: nbrOfArrays.ChromosomalModel
Aliases: nbrOfArrays.ChromosomalModel ChromosomalModel.nbrOfArrays nbrOfArrays.ChromosomalModel nbrOfArrays,ChromosomalModel-method
Keywords: internal methods
Description: Gets the number of arrays
URL: ../../../library/aroma.core/html/nbrOfArrays.ChromosomalModel.html

Entry: nbrOfArrays.Explorer
Aliases: nbrOfArrays.Explorer Explorer.nbrOfArrays nbrOfArrays.Explorer nbrOfArrays,Explorer-method
Keywords: internal methods
Description: Gets the total number of arrays
URL: ../../../library/aroma.core/html/nbrOfArrays.Explorer.html

Entry: nbrOfChipTypes.AromaMicroarrayDataSetTuple
Aliases: nbrOfChipTypes.AromaMicroarrayDataSetTuple AromaMicroarrayDataSetTuple.nbrOfChipTypes nbrOfChipTypes.AromaMicroarrayDataSetTuple nbrOfChipTypes,AromaMicroarrayDataSetTuple-method
Keywords: internal methods
Description: Gets the number of chip types
URL: ../../../library/aroma.core/html/nbrOfChipTypes.AromaMicroarrayDataSetTuple.html

Entry: nbrOfChipTypes.ChromosomalModel
Aliases: nbrOfChipTypes.ChromosomalModel ChromosomalModel.nbrOfChipTypes nbrOfChipTypes.ChromosomalModel nbrOfChipTypes,ChromosomalModel-method
Keywords: internal methods
Description: Gets the number of chip types
URL: ../../../library/aroma.core/html/nbrOfChipTypes.ChromosomalModel.html

Entry: patchPackage
Aliases: patchPackage.default patchPackage
Keywords: internal
Description: Applies patches for a specific package
URL: ../../../library/aroma.core/html/patchPackage.html

Entry: process.AromaTransform
Aliases: process.AromaTransform AromaTransform.process process.AromaTransform process,AromaTransform-method
Keywords: internal methods
Description: Processes the data set
URL: ../../../library/aroma.core/html/process.AromaTransform.html

Entry: process.ChromosomeExplorer
Aliases: process.ChromosomeExplorer ChromosomeExplorer.process process.ChromosomeExplorer process,ChromosomeExplorer-method
Keywords: internal methods
Description: Generates image files, scripts and dynamic pages for the explorer
URL: ../../../library/aroma.core/html/process.ChromosomeExplorer.html

Entry: process.Explorer
Aliases: process.Explorer Explorer.process process.Explorer process,Explorer-method
Keywords: internal methods
Description: Generates image files, scripts and dynamic pages for the explorer
URL: ../../../library/aroma.core/html/process.Explorer.html

Entry: processTime
Aliases: processTime.default processTime
Keywords: programming internal
Description: Gets the running time of the R process and its children processes
URL: ../../../library/aroma.core/html/processTime.html

Entry: readFooter.AromaTabularBinaryFile
Aliases: readFooter.AromaTabularBinaryFile AromaTabularBinaryFile.readFooter readFooter.AromaTabularBinaryFile readFooter,AromaTabularBinaryFile-method
Keywords: internal methods IO programming
Description: Reads the file footer in XML format into a named nested list
URL: ../../../library/aroma.core/html/readFooter.AromaTabularBinaryFile.html

Entry: segmentByCBS.RawGenomicSignals
Aliases: segmentByCBS.RawGenomicSignals RawGenomicSignals.segmentByCBS segmentByCBS.RawGenomicSignals segmentByCBS,RawGenomicSignals-method
Keywords: internal methods IO
Description: Segment copy numbers using the CBS method
URL: ../../../library/aroma.core/html/segmentByCBS.RawGenomicSignals.html

Entry: segmentByGLAD.RawGenomicSignals
Aliases: segmentByGLAD.RawGenomicSignals RawGenomicSignals.segmentByGLAD segmentByGLAD.RawGenomicSignals segmentByGLAD,RawGenomicSignals-method
Keywords: internal methods IO
Description: Segment copy numbers using the GLAD method
URL: ../../../library/aroma.core/html/segmentByGLAD.RawGenomicSignals.html

Entry: segmentByHaarSeg.RawGenomicSignals
Aliases: segmentByHaarSeg.RawGenomicSignals RawGenomicSignals.segmentByHaarSeg segmentByHaarSeg.RawGenomicSignals segmentByHaarSeg,RawGenomicSignals-method
Keywords: internal methods IO
Description: Segment copy numbers using the HaarSeg method
URL: ../../../library/aroma.core/html/segmentByHaarSeg.RawGenomicSignals.html

Entry: setAlias.Explorer
Aliases: setAlias.Explorer Explorer.setAlias setAlias.Explorer setAlias,Explorer-method
Keywords: internal methods
Description: Sets the alias of the output set
URL: ../../../library/aroma.core/html/setAlias.Explorer.html

Entry: setArrays.ChromosomeExplorer
Aliases: setArrays.ChromosomeExplorer ChromosomeExplorer.setArrays setArrays.ChromosomeExplorer setArrays,ChromosomeExplorer-method
Keywords: internal methods
Description: Sets the arrays
URL: ../../../library/aroma.core/html/setArrays.ChromosomeExplorer.html

Entry: setArrays.Explorer
Aliases: setArrays.Explorer Explorer.setArrays setArrays.Explorer setArrays,Explorer-method
Keywords: internal methods
Description: Sets the arrays
URL: ../../../library/aroma.core/html/setArrays.Explorer.html

Entry: updateSamplesFile.ChromosomeExplorer
Aliases: updateSamplesFile.ChromosomeExplorer ChromosomeExplorer.updateSamplesFile updateSamplesFile.ChromosomeExplorer updateSamplesFile,ChromosomeExplorer-method
Keywords: internal methods
Description: Updates the samples.js file
URL: ../../../library/aroma.core/html/updateSamplesFile.ChromosomeExplorer.html

Entry: writeFooter.AromaTabularBinaryFile
Aliases: writeFooter.AromaTabularBinaryFile AromaTabularBinaryFile.writeFooter writeFooter.AromaTabularBinaryFile writeFooter,AromaTabularBinaryFile-method
Keywords: internal methods IO programming
Description: Writes a named nested list to the file footer in XML format
URL: ../../../library/aroma.core/html/writeFooter.AromaTabularBinaryFile.html
