| # |
Man page
|
| $.RichDataFrame |
Man page
|
| $<-.RichDataFrame |
Man page
|
| *.CopyNumberRegions |
Man page
|
| *.RawGenomicSignals |
Man page
|
| +.CopyNumberRegions |
Man page
|
| +.RawGenomicSignals |
Man page
|
| -.CopyNumberRegions |
Man page
|
| -.RawGenomicSignals |
Man page
|
| .loadSettings |
Source code
|
| .onAttach |
Source code
|
| .onLoad |
Source code
|
| .requireBiocPackage |
Source code
|
| .setupAromaCore |
Source code
|
| .stop_if_not |
Source code
|
| / |
Man page
|
| AbstractCNData |
Man page
|
| AbstractPSCNData |
Man page
|
| AromaCellCpgFile |
Man page
|
| AromaCellPositionFile |
Man page
|
| AromaCellSequenceFile |
Man page
|
| AromaCellTabularBinaryFile |
Man page
|
| AromaCore |
Man page
|
| AromaGenomeTextFile |
Man page
|
| AromaMicroarrayDataFile |
Man page
|
| AromaMicroarrayDataSet |
Man page
|
| AromaMicroarrayDataSetTuple |
Man page
|
| AromaMicroarrayDataSetTuple.nbrOfChipTypes |
Man page
|
| AromaMicroarrayTabularBinaryFile |
Man page
|
| AromaPackage |
Man page
|
| AromaPlatform |
Man page
|
| AromaPlatformInterface |
Man page
|
| AromaPlatformInterface.getAromaPlatform |
Man page
|
| AromaPlatformInterface.getAromaUflFile |
Man page
|
| AromaPlatformInterface.getAromaUgpFile |
Man page
|
| AromaPlatformInterface.getChipType |
Man page
|
| AromaPlatformInterface.getPlatform |
Man page
|
| AromaPlatformInterface.getUnitAnnotationDataFile |
Man page
|
| AromaPlatformInterface.getUnitNamesFile |
Man page
|
| AromaPlatformInterface.getUnitTypesFile |
Man page
|
| AromaPlatformInterface.isCompatibleWith |
Man page
|
| AromaRepository |
Man page
|
| AromaRepository.downloadChipTypeFile |
Man page
|
| AromaRepository.downloadFile |
Man page
|
| AromaRepository.listFiles |
Man page
|
| AromaSettings |
Man page
|
| AromaTabularBinaryFile |
Man page
|
| AromaTabularBinaryFile$allocate |
Man page
|
| AromaTabularBinaryFile.allocate |
Man page
|
| AromaTabularBinaryFile.readFooter |
Man page
|
| AromaTabularBinaryFile.writeFooter |
Man page
|
| AromaTabularBinarySet |
Man page
|
| AromaTransform |
Man page
|
| AromaTransform.findFilesTodo |
Man page
|
| AromaTransform.getFullName |
Man page
|
| AromaTransform.getInputDataSet |
Man page
|
| AromaTransform.getName |
Man page
|
| AromaTransform.getOutputDataSet |
Man page
|
| AromaTransform.getPath |
Man page
|
| AromaTransform.getRootPath |
Man page
|
| AromaTransform.getTags |
Man page
|
| AromaTransform.isDone |
Man page
|
| AromaTransform.process |
Man page
|
| AromaUcscGenomeTextFile |
Man page
|
| AromaUflFile |
Man page
|
| AromaUgcFile |
Man page
|
| AromaUgpFile |
Man page
|
| AromaUnitCallFile |
Man page
|
| AromaUnitCallSet |
Man page
|
| AromaUnitChromosomeTabularBinaryFile |
Man page
|
| AromaUnitFracBCnBinaryFile |
Man page
|
| AromaUnitFracBCnBinarySet |
Man page
|
| AromaUnitGcContentFile |
Man page
|
| AromaUnitGenotypeCallFile |
Man page
|
| AromaUnitGenotypeCallSet |
Man page
|
| AromaUnitPscnBinaryFile |
Man page
|
| AromaUnitPscnBinarySet |
Man page
|
| AromaUnitSignalBinaryFile |
Man page
|
| AromaUnitSignalBinaryFile.writeDataFrame |
Man page
|
| AromaUnitSignalBinarySet |
Man page
|
| AromaUnitSignalBinarySet.writeDataFrame |
Man page
|
| AromaUnitTabularBinaryFile |
Man page
|
| AromaUnitTabularBinaryFile.writeDataFrame |
Man page
|
| AromaUnitTotalCnBinaryFile |
Man page
|
| AromaUnitTotalCnBinaryFileList |
Man page
|
| AromaUnitTotalCnBinarySet |
Man page
|
| AromaUnitTotalCnBinarySetTuple |
Man page
|
| AromaUnitTypesFile |
Man page
|
| BinnedScatter |
Man page
|
| CacheKeyInterface |
Man page
|
| CacheKeyInterface.getCacheKey |
Man page
|
| CbsModel |
Man page
|
| CbsSegmentationDataFile |
Man page
|
| CbsSegmentationDataSet |
Man page
|
| ChromosomalModel |
Man page
|
| ChromosomalModel.getChipType |
Man page
|
| ChromosomalModel.getChromosomes |
Man page
|
| ChromosomalModel.getNames |
Man page
|
| ChromosomalModel.nbrOfArrays |
Man page
|
| ChromosomalModel.nbrOfChipTypes |
Man page
|
| ChromosomeExplorer |
Man page
|
| ChromosomeExplorer.getChromosomes |
Man page
|
| ChromosomeExplorer.getModel |
Man page
|
| ChromosomeExplorer.process |
Man page
|
| ChromosomeExplorer.setArrays |
Man page
|
| ChromosomeExplorer.updateSetupExplorerFile |
Man page
|
| CopyNumberChromosomalModel |
Man page
|
| CopyNumberChromosomalModel.estimateSds |
Man page
|
| CopyNumberChromosomalModel.extractRawCopyNumbers |
Man page
|
| CopyNumberChromosomalModel.fit |
Man page
|
| CopyNumberDataFile |
Man page
|
| CopyNumberDataSet |
Man page
|
| CopyNumberDataSetTuple |
Man page
|
| CopyNumberOutliers |
Man page
|
| CopyNumberRegions |
Man page
|
| CopyNumberSegmentationModel |
Man page
|
| CopyNumberSegmentationModel.fit |
Man page
|
| DEFUNCT |
Man page
|
| DEPRECATED |
Man page
|
| Explorer |
Man page
|
| Explorer.display |
Man page
|
| Explorer.getAlias |
Man page
|
| Explorer.getName |
Man page
|
| Explorer.getNames |
Man page
|
| Explorer.getPath |
Man page
|
| Explorer.getRootPath |
Man page
|
| Explorer.getTags |
Man page
|
| Explorer.nbrOfArrays |
Man page
|
| Explorer.process |
Man page
|
| Explorer.setAlias |
Man page
|
| Explorer.setArrays |
Man page
|
| FileCacheKeyInterface |
Man page
|
| FileCacheKeyInterface.getCacheKey |
Man page
|
| GladModel |
Man page
|
| HaarSegModel |
Man page
|
| MISC. |
Man page
|
| Non-documented objects |
Man page
|
| NonPairedPSCNData |
Man page
|
| PairedPSCNData |
Man page
|
| PairedPSCNData.plotTracks |
Man page
|
| ParametersInterface |
Man page
|
| ParametersInterface.getParameters |
Man page
|
| ParametersInterface.getParametersAsString |
Man page
|
| RasterImage |
Man page
|
| RawAlleleBFractions |
Man page
|
| RawCopyNumberModel |
Man page
|
| RawCopyNumbers |
Man page
|
| RawGenomicSignals |
Man page
|
| RawGenomicSignals.estimateStandardDeviation |
Man page
|
| RawGenomicSignals.segmentByCBS |
Man page
|
| RawGenomicSignals.segmentByGLAD |
Man page
|
| RawGenomicSignals.segmentByHaarSeg |
Man page
|
| RawGenomicSignals.segmentByMPCBS |
Man page
|
| RawMirroredAlleleBFractions |
Man page
|
| RawSequenceReads |
Man page
|
| RichDataFrame |
Man page
|
| SampleAnnotationFile |
Man page
|
| SampleAnnotationSet |
Man page
|
| SegmentationDataFile |
Man page
|
| SegmentationDataSet |
Man page
|
| SegmentedAlleleBFractions |
Man page
|
| SegmentedCopyNumbers |
Man page
|
| SegmentedGenomicSignalsInterface |
Man page
|
| TextUnitNamesFile |
Man page
|
| UnitAnnotationDataFile |
Man page
|
| UnitNamesFile |
Man page
|
| UnitNamesFile.indexOf |
Man page
|
| UnitTypesFile |
Man page
|
| [.AromaTabularBinaryFile |
Man page
|
| [.RasterImage |
Man page
|
| [.RichDataFrame |
Man page
|
| [<-.AromaTabularBinaryFile |
Man page
|
| [[.AromaTabularBinaryFile |
Man page
|
| [[.RichDataFrame |
Man page
|
| [[<-.RichDataFrame |
Man page
|
| addBy |
Man page
|
| addBy.RawGenomicSignals |
Man page
|
| addIncludes |
Man page
|
| addIncludes.Explorer |
Man page
|
| addIndexFile |
Man page
|
| addIndexFile.ChromosomeExplorer |
Man page
|
| addIndexFile.Explorer |
Man page
|
| addLocusFields |
Man page
|
| addLocusFields.RawGenomicSignals |
Man page
|
| allocate |
Man page
|
| allocate,AromaTabularBinaryFile-method |
Man page
|
| allocate.AromaCellCpgFile |
Man page
|
| allocate.AromaCellPositionFile |
Man page
|
| allocate.AromaCellSequenceFile |
Man page
|
| allocate.AromaMicroarrayTabularBinaryFile |
Man page
|
| allocate.AromaTabularBinaryFile |
Man page
|
| allocate.AromaUflFile |
Man page
|
| allocate.AromaUgpFile |
Man page
|
| allocate.AromaUnitCallFile |
Man page
|
| allocate.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| allocate.AromaUnitGenotypeCallFile |
Man page
|
| allocate.AromaUnitPscnBinaryFile |
Man page
|
| allocate.AromaUnitSignalBinaryFile |
Man page
|
| allocate.AromaUnitTypesFile |
Man page
|
| allocateFromUnitAnnotationDataFile |
Man page
|
| allocateFromUnitAnnotationDataFile.AromaUnitSignalBinaryFile |
Man page
|
| allocateFromUnitAnnotationDataFile.AromaUnitTabularBinaryFile |
Man page
|
| allocateFromUnitNamesFile |
Man page
|
| allocateFromUnitNamesFile.AromaUnitSignalBinaryFile |
Man page
|
| allocateFromUnitNamesFile.AromaUnitTabularBinaryFile |
Man page
|
| append |
Man page
|
| append.CopyNumberRegions |
Man page
|
| append.RawGenomicSignals |
Man page
|
| applyBinaryOperator |
Man page
|
| applyBinaryOperator.RawGenomicSignals |
Man page
|
| applyRegions |
Man page
|
| applyRegions.CopyNumberOutliers |
Man page
|
| applyRows |
Man page
|
| applyRows.CopyNumberRegions |
Man page
|
| applyTo |
Man page
|
| applyTo.SampleAnnotationFile |
Man page
|
| aroma.core |
Man page
|
| aroma.core-package |
Man page
|
| aromaSettings |
Man page
|
| as.AromaMicroarrayDataSetList |
Man page
|
| as.AromaMicroarrayDataSetList.AromaMicroarrayDataSet |
Man page
|
| as.AromaMicroarrayDataSetTuple |
Man page
|
| as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSet |
Man page
|
| as.AromaMicroarrayDataSetTuple.AromaMicroarrayDataSetTuple |
Man page
|
| as.AromaUnitTotalCnBinarySetTuple |
Man page
|
| as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySet |
Man page
|
| as.AromaUnitTotalCnBinarySetTuple.AromaUnitTotalCnBinarySetTuple |
Man page
|
| as.CopyNumberDataFile |
Man page
|
| as.CopyNumberDataFile.CopyNumberDataFile |
Man page
|
| as.CopyNumberDataSet |
Man page
|
| as.CopyNumberDataSet.CopyNumberDataSet |
Man page
|
| as.CopyNumberDataSetTuple |
Man page
|
| as.CopyNumberDataSetTuple.AromaUnitTotalCnBinarySet |
Man page
|
| as.CopyNumberDataSetTuple.CopyNumberDataSetTuple |
Man page
|
| as.CopyNumberDataSetTuple.list |
Man page
|
| as.GrayscaleImage |
Man page
|
| as.GrayscaleImage.matrix |
Man page
|
| as.NonPairedPSCNData |
Man page
|
| as.NonPairedPSCNData.NonPairedPSCNData |
Man page
|
| as.NonPairedPSCNData.data.frame |
Man page
|
| as.PairedPSCNData |
Man page
|
| as.PairedPSCNData.NonPairedPSCNData |
Man page
|
| as.PairedPSCNData.PairedPSCNData |
Man page
|
| as.PairedPSCNData.data.frame |
Man page
|
| as.TrueColorImage |
Man page
|
| as.TrueColorImage.Image |
Man page
|
| as.TrueColorImage.matrix |
Man page
|
| as.character.AromaMicroarrayDataSetTuple |
Man page
|
| as.character.AromaMicroarrayTabularBinaryFile |
Man page
|
| as.character.AromaPlatform |
Man page
|
| as.character.AromaTabularBinaryFile |
Man page
|
| as.character.AromaTransform |
Man page
|
| as.character.AromaUnitSignalBinaryFile |
Man page
|
| as.character.ChromosomalModel |
Man page
|
| as.character.ChromosomeExplorer |
Man page
|
| as.character.CopyNumberChromosomalModel |
Man page
|
| as.character.CopyNumberOutliers |
Man page
|
| as.character.CopyNumberRegions |
Man page
|
| as.character.Explorer |
Man page
|
| as.character.RasterImage |
Man page
|
| as.character.RawGenomicSignals |
Man page
|
| as.character.SegmentationDataSet |
Man page
|
| as.character.TextUnitNamesFile |
Man page
|
| as.data.frame.CopyNumberOutliers |
Man page
|
| as.data.frame.CopyNumberRegions |
Man page
|
| as.data.frame.RawCopyNumbers |
Man page
|
| as.data.frame.RawGenomicSignals |
Man page
|
| as.data.frame.RichDataFrame |
Man page
|
| as.data.frame.SegmentedGenomicSignalsInterface |
Man page
|
| as.list.RichDataFrame |
Man page
|
| asMatrixOfFiles |
Man page
|
| asMatrixOfFiles.AromaMicroarrayDataSetTuple |
Man page
|
| asThis |
Man page
|
| asThis.BasicObject |
Man page
|
| asThis.Object |
Man page
|
| assertOneChromosome |
Man page
|
| assertOneChromosome.RawGenomicSignals |
Man page
|
| backtransformGenotypeCone |
Man page
|
| backtransformGenotypeCone.matrix |
Man page
|
| backtransformMultiDimensionalCone |
Man page
|
| backtransformMultiDimensionalCone.matrix |
Man page
|
| barSequence |
Man page
|
| barSequence.ProbePositionEffects |
Man page
|
| binScatter |
Man page
|
| binScatter.matrix |
Man page
|
| binnedSmoothing |
Man page
|
| binnedSmoothing.RawGenomicSignals |
Man page
|
| binnedSmoothing.numeric |
Man page
|
| binnedSmoothingByField |
Man page
|
| binnedSmoothingByField.RawGenomicSignals |
Man page
|
| binnedSmoothingByState |
Man page
|
| binnedSmoothingByState.SegmentedGenomicSignalsInterface |
Man page
|
| binnedSums |
Man page
|
| binnedSums.RawSequenceReads |
Man page
|
| byChipType |
Man page
|
| byChipType.AromaCellTabularBinaryFile |
Man page
|
| byChipType.AromaMicroarrayTabularBinaryFile |
Man page
|
| byChipType.AromaUnitTabularBinaryFile |
Man page
|
| byChipType.UnitAnnotationDataFile |
Man page
|
| byGenome |
Man page
|
| byGenome.AromaGenomeTextFile |
Man page
|
| byName.AromaPlatform |
Man page
|
| byName.AromaUnitFracBCnBinarySet |
Man page
|
| byName.AromaUnitGenotypeCallSet |
Man page
|
| byName.AromaUnitPscnBinarySet |
Man page
|
| byName.AromaUnitSignalBinarySet |
Man page
|
| byName.AromaUnitTotalCnBinarySet |
Man page
|
| byName.CbsSegmentationDataSet |
Man page
|
| byPath.AromaMicroarrayDataSetTuple |
Man page
|
| byPath.AromaUnitCallSet |
Man page
|
| byPath.AromaUnitGenotypeCallSet |
Man page
|
| byPath.CbsSegmentationDataSet |
Man page
|
| byPath.SegmentationDataSet |
Man page
|
| byPathnames |
Man page
|
| byPathnames.SampleAnnotationSet |
Man page
|
| calcMargins |
Man page
|
| calcMargins.matrix |
Man page
|
| calculateAverageColumnAcrossFiles |
Man page
|
| calculateAverageColumnAcrossFiles.GenericTabularFileSet |
Man page
|
| calculateChromosomeStatistics |
Man page
|
| calculateChromosomeStatistics.CopyNumberChromosomalModel |
Man page
|
| calculateRatios |
Man page
|
| calculateRatios.CopyNumberChromosomalModel |
Man page
|
| callNaiveGenotypes |
Man page
|
| callNaiveGenotypes.NonPairedPSCNData |
Man page
|
| callNaiveGenotypes.PairedPSCNData |
Man page
|
| callSNPs |
Man page
|
| callSNPs.AbstractPSCNData |
Man page
|
| callSegmentationOutliers |
Man page
|
| callSegmentationOutliers.NonPairedPSCNData |
Man page
|
| callSegmentationOutliers.PairedPSCNData |
Man page
|
| cat |
Man page
|
| clearCache.AromaRepository |
Man page
|
| clearCache.RawGenomicSignals |
Man page
|
| clone.RawGenomicSignals |
Man page
|
| cnRange |
Man page
|
| cnRange.RawCopyNumbers |
Man page
|
| colApply |
Man page
|
| colApply.AromaTabularBinaryFile |
Man page
|
| colBinnedSmoothing |
Man page
|
| colBinnedSmoothing.matrix |
Man page
|
| colGaussianSmoothing |
Man page
|
| colGaussianSmoothing.matrix |
Man page
|
| colKernelSmoothing |
Man page
|
| colKernelSmoothing.matrix |
Man page
|
| colMeans |
Man page
Source code
|
| colMeans.AromaTabularBinaryFile |
Man page
|
| colMeans.default |
Man page
|
| colStats |
Man page
|
| colStats.AromaTabularBinaryFile |
Man page
|
| colSums |
Man page
Source code
|
| colSums.AromaTabularBinaryFile |
Man page
|
| colSums.default |
Man page
|
| colorize |
Man page
|
| colorize.Image |
Man page
|
| colorize.RasterImage |
Man page
|
| convertTable |
Man page
|
| convertTable.default |
Man page
|
| countBases |
Man page
|
| countBases.AromaCellSequenceFile |
Man page
|
| countBasesInternal |
Man page
|
| countBasesInternal.AromaCellSequenceFile |
Man page
|
| createImage |
Man page
|
| createImage.matrix |
Man page
|
| dim.RichDataFrame |
Man page
|
| dimnames<-.AromaTabularBinaryFile |
Man page
|
| display |
Man page
|
| display,Explorer-method |
Man page
|
| display.ChromosomeExplorer |
Man page
|
| display.Explorer |
Man page
|
| display.Image |
Man page
|
| display.RasterImage |
Man page
|
| divideBy |
Man page
|
| divideBy.RawGenomicSignals |
Man page
|
| doCBS |
Man page
|
| doCBS.CopyNumberDataSet |
Man page
|
| doCBS.CopyNumberDataSetTuple |
Man page
|
| doCBS.character |
Man page
|
| doCBS.default |
Man page
|
| downloadACC |
Man page
|
| downloadACC.AromaRepository |
Man page
|
| downloadACM |
Man page
|
| downloadACM.AromaRepository |
Man page
|
| downloadACP |
Man page
|
| downloadACP.AromaRepository |
Man page
|
| downloadACS |
Man page
|
| downloadACS.AromaRepository |
Man page
|
| downloadAll |
Man page
|
| downloadAll.AromaRepository |
Man page
|
| downloadCDF |
Man page
|
| downloadCDF.AromaRepository |
Man page
|
| downloadChipTypeFile |
Man page
|
| downloadChipTypeFile,AromaRepository-method |
Man page
|
| downloadChipTypeFile.AromaRepository |
Man page
|
| downloadFile,AromaRepository-method |
Man page
|
| downloadFile.AromaRepository |
Man page
|
| downloadProbeSeqsTXT |
Man page
|
| downloadProbeSeqsTXT.AromaRepository |
Man page
|
| downloadTXT |
Man page
|
| downloadTXT.AromaRepository |
Man page
|
| downloadUFL |
Man page
|
| downloadUFL.AromaRepository |
Man page
|
| downloadUGC |
Man page
|
| downloadUGC.AromaRepository |
Man page
|
| downloadUGP |
Man page
|
| downloadUGP.AromaRepository |
Man page
|
| drawCnRegions |
Man page
|
| drawCnRegions.DNAcopy |
Man page
|
| drawCnRegions.HaarSeg |
Man page
|
| drawCnRegions.MPCBS |
Man page
|
| drawCnRegions.profileCGH |
Man page
|
| drawCytoband |
Man page
|
| drawCytoband.ChromosomalModel |
Man page
|
| drawCytoband.profileCGH |
Man page
|
| drawCytoband2 |
Man page
|
| drawCytoband2.default |
Man page
|
| drawDensity |
Man page
|
| drawDensity.CopyNumberRegions |
Man page
|
| drawDensity.RawGenomicSignals |
Man page
|
| drawExtraAnnotations |
Man page
|
| drawExtraAnnotations.default |
Man page
|
| drawExtraAnnotations.profileCGH |
Man page
|
| drawLevels |
Man page
|
| drawLevels.CopyNumberOutliers |
Man page
|
| drawLevels.CopyNumberRegions |
Man page
|
| dropAlpha |
Man page
|
| dropAlpha.RasterImage |
Man page
|
| dropRootPathTags.default |
Man page
|
| dropSegmentationOutliers |
Man page
|
| dropSegmentationOutliers.NonPairedPSCNData |
Man page
|
| dropSegmentationOutliers.PairedPSCNData |
Man page
|
| dropVirtualColumn |
Man page
|
| dropVirtualColumn.RichDataFrame |
Man page
|
| equals.AromaPlatform |
Man page
|
| equals.CopyNumberRegions |
Man page
|
| estimateSds |
Man page
|
| estimateSds,CopyNumberChromosomalModel-method |
Man page
|
| estimateSds.CopyNumberChromosomalModel |
Man page
|
| estimateStandardDeviation |
Man page
|
| estimateStandardDeviation,RawGenomicSignals-method |
Man page
|
| estimateStandardDeviation.RawGenomicSignals |
Man page
|
| exportAromaUnitPscnBinarySet |
Man page
|
| exportAromaUnitPscnBinarySet.AromaUnitTotalCnBinarySet |
Man page
|
| exportAromaUnitPscnBinarySet.list |
Man page
|
| exportFracBDiffSet |
Man page
|
| exportFracBDiffSet.AromaUnitFracBCnBinarySet |
Man page
|
| exportTotalCnRatioSet |
Man page
|
| exportTotalCnRatioSet.AromaUnitTotalCnBinarySet |
Man page
|
| extractByChromosome |
Man page
|
| extractByChromosome.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| extractByReferenceName |
Man page
|
| extractByReferenceName.SegmentationDataSet |
Man page
|
| extractBySampleName |
Man page
|
| extractBySampleName.SegmentationDataSet |
Man page
|
| extractCNRs |
Man page
|
| extractCNRs.default |
Man page
|
| extractCallArray |
Man page
|
| extractCallArray.AromaUnitCallFile |
Man page
|
| extractCallArray.AromaUnitCallSet |
Man page
|
| extractCalls |
Man page
|
| extractCalls.AromaUnitCallFile |
Man page
|
| extractCalls.AromaUnitCallSet |
Man page
|
| extractChromosome |
Man page
|
| extractChromosome.RawGenomicSignals |
Man page
|
| extractChromosomes |
Man page
|
| extractChromosomes.RawGenomicSignals |
Man page
|
| extractCopyNumberOutliers |
Man page
|
| extractCopyNumberOutliers.DNAcopy |
Man page
|
| extractCopyNumberOutliers.profileCGH |
Man page
|
| extractCopyNumberRegions |
Man page
|
| extractCopyNumberRegions.DNAcopy |
Man page
|
| extractCopyNumberRegions.HaarSeg |
Man page
|
| extractCopyNumberRegions.MPCBS |
Man page
|
| extractCopyNumberRegions.SegmentationDataFile |
Man page
|
| extractCopyNumberRegions.SegmentationDataSet |
Man page
|
| extractCopyNumberRegions.default |
Man page
|
| extractCopyNumberRegions.profileCGH |
Man page
|
| extractDataForSegmentation |
Man page
|
| extractDataForSegmentation.RawGenomicSignals |
Man page
|
| extractGenotypeMatrix |
Man page
|
| extractGenotypeMatrix.AromaUnitCallSet |
Man page
|
| extractGenotypeMatrix.AromaUnitGenotypeCallFile |
Man page
|
| extractGenotypes |
Man page
|
| extractGenotypes.AromaUnitGenotypeCallFile |
Man page
|
| extractGenotypes.AromaUnitGenotypeCallSet |
Man page
|
| extractIGV |
Man page
|
| extractIGV.CopyNumberRegions |
Man page
|
| extractMatrix.AromaUnitCallFile |
Man page
|
| extractMatrix.AromaUnitSignalBinaryFile |
Man page
|
| extractMergedRawCopyNumbers |
Man page
|
| extractMergedRawCopyNumbers.AromaUnitTotalCnBinaryFileList |
Man page
|
| extractNonPairedPSCNData |
Man page
|
| extractNonPairedPSCNData.PairedPSCNData |
Man page
|
| extractOld |
Man page
|
| extractOld.AromaMicroarrayDataSetTuple |
Man page
|
| extractPSCNArray |
Man page
|
| extractPSCNArray.AromaUnitTotalCnBinaryFile |
Man page
|
| extractPSCNArray.AromaUnitTotalCnBinarySet |
Man page
|
| extractPSCNMatrix |
Man page
|
| extractPSCNMatrix.AromaUnitTotalCnBinaryFile |
Man page
|
| extractRawAlleleBFractions |
Man page
|
| extractRawAlleleBFractions.AromaUnitFracBCnBinaryFile |
Man page
|
| extractRawAlleleBFractions.default |
Man page
|
| extractRawCNs |
Man page
|
| extractRawCNs.default |
Man page
|
| extractRawCopyNumbers |
Man page
|
| extractRawCopyNumbers,CopyNumberChromosomalModel-method |
Man page
|
| extractRawCopyNumbers.AromaUnitPscnBinaryFile |
Man page
|
| extractRawCopyNumbers.AromaUnitTotalCnBinaryFile |
Man page
|
| extractRawCopyNumbers.AromaUnitTotalCnBinaryFileList |
Man page
|
| extractRawCopyNumbers.CopyNumberChromosomalModel |
Man page
|
| extractRawCopyNumbers.DNAcopy |
Man page
|
| extractRawCopyNumbers.HaarSeg |
Man page
|
| extractRawCopyNumbers.RawCopyNumbers |
Man page
|
| extractRawCopyNumbers.RawSequenceReads |
Man page
|
| extractRawCopyNumbers.default |
Man page
|
| extractRawCopyNumbers.profileCGH |
Man page
|
| extractRawGenomicSignals |
Man page
|
| extractRawGenomicSignals.AromaUnitSignalBinaryFile |
Man page
|
| extractRawGenomicSignals.AromaUnitTotalCnBinaryFileList |
Man page
|
| extractRawGenomicSignals.default |
Man page
|
| extractRawMirroredAlleleBFractions |
Man page
|
| extractRawMirroredAlleleBFractions.RawAlleleBFractions |
Man page
|
| extractRawMirroredAlleleBFractions.default |
Man page
|
| extractRegion |
Man page
|
| extractRegion.RawGenomicSignals |
Man page
|
| extractRegions |
Man page
|
| extractRegions.RawGenomicSignals |
Man page
|
| extractSubset |
Man page
|
| extractSubset.RawGenomicSignals |
Man page
|
| extractSubsetByState |
Man page
|
| extractSubsetByState.SegmentedGenomicSignalsInterface |
Man page
|
| findAnnotationData |
Man page
|
| findAnnotationData.default |
Man page
|
| findAnnotationDataByChipType |
Man page
|
| findAnnotationDataByChipType.AromaRepository |
Man page
|
| findAnnotationDataByChipType.default |
Man page
|
| findByChipType |
Man page
|
| findByChipType.AromaMicroarrayTabularBinaryFile |
Man page
|
| findByChipType.TextUnitNamesFile |
Man page
|
| findByGenome |
Man page
|
| findByGenome.AromaGenomeTextFile |
Man page
|
| findByGenome.AromaUcscGenomeTextFile |
Man page
|
| findByName.AromaUnitCallSet |
Man page
|
| findByName.AromaUnitSignalBinarySet |
Man page
|
| findChangePointsByState |
Man page
|
| findChangePointsByState.SegmentedGenomicSignalsInterface |
Man page
|
| findFilesTodo |
Man page
|
| findFilesTodo,AromaTransform-method |
Man page
|
| findFilesTodo.AromaTransform |
Man page
|
| findLargeGaps |
Man page
|
| findLargeGaps.AbstractCNData |
Man page
|
| findPngDevice |
Man page
|
| findPngDevice.default |
Man page
|
| findSAFs |
Man page
|
| findSAFs.SampleAnnotationSet |
Man page
|
| findUnitNamesFile |
Man page
|
| findUnitNamesFile.AromaPlatform |
Man page
|
| findUnitTypesFile |
Man page
|
| findUnitTypesFile.AromaPlatform |
Man page
|
| findUnitsTodo |
Man page
|
| findUnitsTodo.AromaUnitCallFile |
Man page
|
| findUnitsTodo.AromaUnitCallSet |
Man page
|
| fit |
Man page
|
| fit,CopyNumberChromosomalModel-method |
Man page
|
| fit,CopyNumberSegmentationModel-method |
Man page
|
| fit.ChromosomalModel |
Man page
|
| fit.CopyNumberChromosomalModel |
Man page
|
| fit.CopyNumberSegmentationModel |
Man page
|
| fit2d |
Man page
|
| fit2d.matrix |
Man page
|
| fitGenotypeCone |
Man page
|
| fitGenotypeCone.matrix |
Man page
|
| fitGenotypeConeByExpectile |
Man page
|
| fitGenotypeConeByExpectile.matrix |
Man page
|
| fitGenotypeConeBySfit |
Man page
|
| fitGenotypeConeBySfit.matrix |
Man page
|
| fitMultiDimensionalCone |
Man page
|
| fitMultiDimensionalCone.matrix |
Man page
|
| fitProbePositionEffects |
Man page
|
| fitProbePositionEffects.numeric |
Man page
|
| fitSplineBlockPolish |
Man page
|
| fitSplineBlockPolish.matrix |
Man page
|
| fitWHLAPLM |
Man page
|
| fitWHLAPLM.matrix |
Man page
|
| fitWHRCModel |
Man page
|
| fitWHRCModel.matrix |
Man page
|
| fitWLAPLM |
Man page
|
| fitWLAPLM.matrix |
Man page
|
| fitWRCModel |
Man page
|
| fitWRCModel.matrix |
Man page
|
| fitWRMA |
Man page
|
| fitWRMA.matrix |
Man page
|
| fixSearchPath |
Man page
|
| fixSearchPath.AromaCore |
Man page
|
| fixSearchPath.AromaPackage |
Man page
|
| fixSearchPathInternal |
Man page
|
| fixSearchPathInternal.AromaPackage |
Man page
|
| fromFile.AromaUnitSignalBinaryFile |
Man page
|
| fromPath |
Man page
|
| fromPath.SampleAnnotationFile |
Man page
|
| fromPath.SampleAnnotationSet |
Man page
|
| gaussKernel |
Man page
Source code
|
| gaussianSmoothing |
Man page
|
| gaussianSmoothing.RawGenomicSignals |
Man page
|
| gaussianSmoothing.matrix |
Man page
|
| gaussianSmoothing.numeric |
Man page
|
| getAM |
Man page
|
| getAM.AromaUnitTotalCnBinaryFile |
Man page
|
| getAlias |
Man page
|
| getAlias,Explorer-method |
Man page
|
| getAlias.ChromosomalModel |
Man page
|
| getAlias.Explorer |
Man page
|
| getAromaFullNameTranslatorSet |
Man page
|
| getAromaFullNameTranslatorSet.AromaMicroarrayDataSet |
Man page
|
| getAromaFullNameTranslatorSet.AromaUnitSignalBinarySet |
Man page
|
| getAromaFullNameTranslatorSet.character |
Man page
|
| getAromaGenomeTextFile |
Man page
|
| getAromaGenomeTextFile.ChromosomalModel |
Man page
|
| getAromaPlatform |
Man page
|
| getAromaPlatform,AromaPlatformInterface-method |
Man page
|
| getAromaPlatform.AromaPlatformInterface |
Man page
|
| getAromaUflFile |
Man page
|
| getAromaUflFile,AromaPlatformInterface-method |
Man page
|
| getAromaUflFile.AromaPlatformInterface |
Man page
|
| getAromaUflFile.UnitAnnotationDataFile |
Man page
|
| getAromaUgpFile |
Man page
|
| getAromaUgpFile,AromaPlatformInterface-method |
Man page
|
| getAromaUgpFile.AromaPlatform |
Man page
|
| getAromaUgpFile.AromaPlatformInterface |
Man page
|
| getAromaUgpFile.AromaUnitSignalBinaryFile |
Man page
|
| getAromaUgpFile.AromaUnitSignalBinarySet |
Man page
|
| getAromaUgpFile.UnitAnnotationDataFile |
Man page
|
| getArrayTuple |
Man page
|
| getArrayTuple.AromaMicroarrayDataSetTuple |
Man page
|
| getArrays |
Man page
|
| getArrays.AromaMicroarrayDataSetTuple |
Man page
|
| getArrays.ChromosomalModel |
Man page
|
| getArrays.Explorer |
Man page
|
| getArraysOfInput |
Man page
|
| getArraysOfInput.ChromosomeExplorer |
Man page
|
| getArraysOfInput.Explorer |
Man page
|
| getAsteriskTags.AromaMicroarrayDataSetTuple |
Man page
|
| getAsteriskTags.AromaTransform |
Man page
|
| getAsteriskTags.ChromosomalModel |
Man page
|
| getAsteriskTags.CopyNumberSegmentationModel |
Man page
|
| getAsteriskTags.Explorer |
Man page
|
| getAsteriskTags.HaarSegModel |
Man page
|
| getAsteriskTags.RawCopyNumberModel |
Man page
|
| getAttributeXY |
Man page
|
| getAttributeXY.AromaMicroarrayDataFile |
Man page
|
| getAverageFile |
Man page
|
| getAverageFile.AromaMicroarrayDataSet |
Man page
|
| getAverageFile.AromaUnitPscnBinarySet |
Man page
|
| getAverageFile.AromaUnitTotalCnBinarySet |
Man page
|
| getBasicField |
Man page
|
| getBasicField.RawGenomicSignals |
Man page
|
| getBytesPerColumn |
Man page
|
| getBytesPerColumn.AromaTabularBinaryFile |
Man page
|
| getCNs |
Man page
|
| getCNs.RawCopyNumbers |
Man page
|
| getCXY |
Man page
|
| getCXY.RawGenomicSignals |
Man page
|
| getCacheKey |
Man page
|
| getCacheKey,CacheKeyInterface-method |
Man page
|
| getCacheKey,FileCacheKeyInterface-method |
Man page
|
| getCacheKey.CacheKeyInterface |
Man page
|
| getCacheKey.FileCacheKeyInterface |
Man page
|
| getChipEffectFiles |
Man page
|
| getChipEffectFiles.ChromosomalModel |
Man page
|
| getChipType |
Man page
|
| getChipType,AromaPlatformInterface-method |
Man page
|
| getChipType,ChromosomalModel-method |
Man page
|
| getChipType.AbstractCNData |
Man page
|
| getChipType.AromaMicroarrayDataFile |
Man page
|
| getChipType.AromaMicroarrayDataSet |
Man page
|
| getChipType.AromaMicroarrayTabularBinaryFile |
Man page
|
| getChipType.AromaPlatformInterface |
Man page
|
| getChipType.AromaUnitSignalBinaryFile |
Man page
|
| getChipType.AromaUnitSignalBinarySet |
Man page
|
| getChipType.AromaUnitTypesFile |
Man page
|
| getChipType.ChromosomalModel |
Man page
|
| getChipType.SegmentationDataSet |
Man page
|
| getChipType.TextUnitNamesFile |
Man page
|
| getChipType.UnitAnnotationDataFile |
Man page
|
| getChipTypes |
Man page
|
| getChipTypes.AromaMicroarrayDataSetTuple |
Man page
|
| getChipTypes.ChromosomalModel |
Man page
|
| getChromosome |
Man page
|
| getChromosome.Arguments |
Man page
|
| getChromosome.RawGenomicSignals |
Man page
|
| getChromosome.SegmentationDataFile |
Man page
|
| getChromosomeLabels |
Man page
|
| getChromosomeLabels.ChromosomeExplorer |
Man page
|
| getChromosomeLength |
Man page
|
| getChromosomeLength.CopyNumberChromosomalModel |
Man page
|
| getChromosomes |
Man page
|
| getChromosomes,ChromosomalModel-method |
Man page
|
| getChromosomes,ChromosomeExplorer-method |
Man page
|
| getChromosomes.Arguments |
Man page
|
| getChromosomes.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getChromosomes.ChromosomalModel |
Man page
|
| getChromosomes.ChromosomeExplorer |
Man page
|
| getChromosomes.CopyNumberRegions |
Man page
|
| getChromosomes.RawGenomicSignals |
Man page
|
| getChromosomes.SegmentationDataSet |
Man page
|
| getCn |
Man page
|
| getCn.RawCopyNumbers |
Man page
|
| getColClasses |
Man page
|
| getColClasses.AromaTabularBinaryFile |
Man page
|
| getColumnNames.AromaCellCpgFile |
Man page
|
| getColumnNames.AromaCellPositionFile |
Man page
|
| getColumnNames.AromaCellSequenceFile |
Man page
|
| getColumnNames.AromaTabularBinaryFile |
Man page
|
| getColumnNames.AromaUflFile |
Man page
|
| getColumnNames.AromaUgpFile |
Man page
|
| getColumnNames.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getColumnNames.AromaUnitGcContentFile |
Man page
|
| getColumnNames.AromaUnitPscnBinaryFile |
Man page
|
| getColumnNames.RichDataFrame |
Man page
|
| getColumnNamesTranslator |
Man page
|
| getColumnNamesTranslator.RichDataFrame |
Man page
|
| getCommonListElements |
Man page
Source code
|
| getDataFileMatrix |
Man page
|
| getDataFileMatrix.CopyNumberChromosomalModel |
Man page
|
| getDefaultColumnNames.AromaCellCpgFile |
Man page
|
| getDefaultColumnNames.AromaCellPositionFile |
Man page
|
| getDefaultColumnNames.AromaCellSequenceFile |
Man page
|
| getDefaultColumnNames.AromaTabularBinaryFile |
Man page
|
| getDefaultColumnNames.AromaUflFile |
Man page
|
| getDefaultColumnNames.AromaUgpFile |
Man page
|
| getDefaultColumnNames.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getDefaultColumnNames.AromaUnitGcContentFile |
Man page
|
| getDefaultColumnNames.AromaUnitPscnBinaryFile |
Man page
|
| getDefaultExtension |
Man page
|
| getDefaultExtension.AromaCellCpgFile |
Man page
|
| getDefaultExtension.AromaCellPositionFile |
Man page
|
| getDefaultExtension.AromaCellSequenceFile |
Man page
|
| getDefaultExtension.AromaUflFile |
Man page
|
| getDefaultExtension.AromaUgpFile |
Man page
|
| getDefaultExtension.UnitAnnotationDataFile |
Man page
|
| getDefaultFullName.AromaMicroarrayDataSet |
Man page
|
| getDefaultFullName.AromaTabularBinarySet |
Man page
|
| getDefaultFullName.SegmentationDataSet |
Man page
|
| getDefaultLocusFields |
Man page
|
| getDefaultLocusFields.RawGenomicSignals |
Man page
|
| getDensity |
Man page
|
| getDensity.CopyNumberRegions |
Man page
|
| getDeviceResolution |
Man page
|
| getDeviceResolution.default |
Man page
|
| getEffects |
Man page
|
| getEffects.ProbePositionEffects |
Man page
|
| getExpectedOutputFiles |
Man page
|
| getExpectedOutputFiles.AromaTransform |
Man page
|
| getExpectedOutputFullnames |
Man page
|
| getExpectedOutputFullnames.AromaTransform |
Man page
|
| getExtensionPattern.AromaCellPositionFile |
Man page
|
| getExtensionPattern.AromaCellSequenceFile |
Man page
|
| getExtensionPattern.AromaUflFile |
Man page
|
| getExtensionPattern.AromaUgpFile |
Man page
|
| getExtensionPattern.AromaUnitGcContentFile |
Man page
|
| getExtensionPattern.AromaUnitSignalBinaryFile |
Man page
|
| getExtensionPattern.SampleAnnotationFile |
Man page
|
| getExtensionPattern.TextUnitNamesFile |
Man page
|
| getFilenameExtension.AromaCellCpgFile |
Man page
|
| getFilenameExtension.AromaCellPositionFile |
Man page
|
| getFilenameExtension.AromaCellSequenceFile |
Man page
|
| getFilenameExtension.AromaMicroarrayTabularBinaryFile |
Man page
|
| getFilenameExtension.AromaUflFile |
Man page
|
| getFilenameExtension.AromaUgpFile |
Man page
|
| getFilenameExtension.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getFilenameExtension.AromaUnitGcContentFile |
Man page
|
| getFilenameExtension.AromaUnitSignalBinaryFile |
Man page
|
| getFilenameExtension.TextUnitNamesFile |
Man page
|
| getFitFunction |
Man page
|
| getFitFunction.CbsModel |
Man page
|
| getFitFunction.CopyNumberSegmentationModel |
Man page
|
| getFitFunction.GladModel |
Man page
|
| getFitFunction.HaarSegModel |
Man page
|
| getFullName,AromaTransform-method |
Man page
|
| getFullName.AromaTransform |
Man page
|
| getFullName.ChromosomalModel |
Man page
|
| getFullName.Explorer |
Man page
|
| getFullName.RichDataFrame |
Man page
|
| getFullNameTranslatorSet |
Man page
|
| getFullNameTranslatorSet.GenericDataFileSet |
Man page
|
| getFullNameTranslatorSet.character |
Man page
|
| getFullNames.AromaMicroarrayDataSetTuple |
Man page
|
| getFullNames.ChromosomalModel |
Man page
|
| getFullNames.ChromosomeExplorer |
Man page
|
| getFullNames.CopyNumberSegmentationModel |
Man page
|
| getGenericSummary |
Man page
|
| getGenericSummary.RichDataFrame |
Man page
|
| getGenome |
Man page
|
| getGenome.ChromosomalModel |
Man page
|
| getGenomeData |
Man page
|
| getGenomeData.ChromosomalModel |
Man page
|
| getGenomeFile |
Man page
|
| getGenomeFile.ChromosomalModel |
Man page
|
| getGenomeVersion |
Man page
|
| getGenomeVersion.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getHeaderParameters |
Man page
|
| getHeaderParameters.TextUnitNamesFile |
Man page
|
| getImage |
Man page
|
| getImage.matrix |
Man page
|
| getImageData |
Man page
|
| getImageData.Image |
Man page
|
| getImageData.RasterImage |
Man page
|
| getIncludePath |
Man page
|
| getIncludePath.Explorer |
Man page
|
| getInputDataSet |
Man page
|
| getInputDataSet,AromaTransform-method |
Man page
|
| getInputDataSet.AromaTransform |
Man page
|
| getLength |
Man page
|
| getLength.CopyNumberRegions |
Man page
|
| getListOfAromaUgpFiles |
Man page
|
| getListOfAromaUgpFiles.ChromosomalModel |
Man page
|
| getListOfChipEffectSets |
Man page
|
| getListOfChipEffectSets.ChromosomalModel |
Man page
|
| getListOfUnitNamesFiles |
Man page
|
| getListOfUnitNamesFiles.AromaUnitTotalCnBinarySetTuple |
Man page
|
| getListOfUnitNamesFiles.ChromosomalModel |
Man page
|
| getListOfUnitTypesFiles |
Man page
|
| getListOfUnitTypesFiles.ChromosomalModel |
Man page
|
| getLociFields |
Man page
|
| getLociFields.RawGenomicSignals |
Man page
|
| getLocusData |
Man page
|
| getLocusData.AbstractCNData |
Man page
|
| getLocusFields |
Man page
|
| getLocusFields.RawGenomicSignals |
Man page
|
| getLog2Ratios |
Man page
|
| getLog2Ratios.CopyNumberSegmentationModel |
Man page
|
| getMainPath |
Man page
|
| getMainPath.Explorer |
Man page
|
| getMaxLengthRepeats |
Man page
|
| getMaxLengthRepeats.AromaCellSequenceFile |
Man page
|
| getMaxNAFraction |
Man page
|
| getMaxNAFraction.CopyNumberChromosomalModel |
Man page
|
| getMeanAt |
Man page
|
| getMeanAt.CopyNumberRegions |
Man page
|
| getModel |
Man page
|
| getModel,ChromosomeExplorer-method |
Man page
|
| getModel.ChromosomeExplorer |
Man page
|
| getName,AromaTransform-method |
Man page
|
| getName,Explorer-method |
Man page
|
| getName.AromaPlatform |
Man page
|
| getName.AromaTransform |
Man page
|
| getName.ChromosomalModel |
Man page
|
| getName.Explorer |
Man page
|
| getName.RawGenomicSignals |
Man page
|
| getName.RichDataFrame |
Man page
|
| getNameOfInput |
Man page
|
| getNameOfInput.ChromosomeExplorer |
Man page
|
| getNameOfInput.Explorer |
Man page
|
| getNames,ChromosomalModel-method |
Man page
|
| getNames,Explorer-method |
Man page
|
| getNames.ChromosomalModel |
Man page
|
| getNames.ChromosomeExplorer |
Man page
|
| getNames.CopyNumberChromosomalModel |
Man page
|
| getNames.Explorer |
Man page
|
| getNumberOfFilesAveraged |
Man page
|
| getNumberOfFilesAveraged.AromaUnitSignalBinaryFile |
Man page
|
| getNumberOfFilesAveraged.CopyNumberDataFile |
Man page
|
| getOption |
Man page
|
| getOptionalArguments |
Man page
|
| getOptionalArguments.CopyNumberChromosomalModel |
Man page
|
| getOutputDataSet |
Man page
|
| getOutputDataSet,AromaTransform-method |
Man page
|
| getOutputDataSet.AromaTransform |
Man page
|
| getOutputDataSet0 |
Man page
|
| getOutputDataSet0.AromaTransform |
Man page
|
| getOutputFiles |
Man page
|
| getOutputFiles.AromaTransform |
Man page
|
| getOutputSet |
Man page
|
| getOutputSet.ChromosomalModel |
Man page
|
| getPairedNames |
Man page
|
| getPairedNames.CopyNumberChromosomalModel |
Man page
|
| getParallelSafe |
Man page
|
| getParallelSafe.Explorer |
Man page
|
| getParameterSets |
Man page
|
| getParameterSets.ParametersInterface |
Man page
|
| getParameters |
Man page
|
| getParameters,ParametersInterface-method |
Man page
|
| getParameters.ParametersInterface |
Man page
|
| getParametersAsString |
Man page
|
| getParametersAsString,ParametersInterface-method |
Man page
|
| getParametersAsString.ParametersInterface |
Man page
|
| getParentName |
Man page
|
| getParentName.GenericDataFile |
Man page
|
| getParentName.GenericDataFileSet |
Man page
|
| getParentPath |
Man page
|
| getParentPath.ChromosomalModel |
Man page
|
| getPath,AromaTransform-method |
Man page
|
| getPath,Explorer-method |
Man page
|
| getPath.AromaTransform |
Man page
|
| getPath.ChromosomalModel |
Man page
|
| getPath.ChromosomeExplorer |
Man page
|
| getPath.Explorer |
Man page
|
| getPatterns |
Man page
|
| getPatterns.SampleAnnotationFile |
Man page
|
| getPhysicalPositions |
Man page
|
| getPhysicalPositions.RawCopyNumbers |
Man page
|
| getPlatform |
Man page
|
| getPlatform,AromaPlatformInterface-method |
Man page
|
| getPlatform.AbstractCNData |
Man page
|
| getPlatform.AromaMicroarrayDataFile |
Man page
|
| getPlatform.AromaMicroarrayDataSet |
Man page
|
| getPlatform.AromaMicroarrayTabularBinaryFile |
Man page
|
| getPlatform.AromaPlatformInterface |
Man page
|
| getPlatform.AromaUnitSignalBinaryFile |
Man page
|
| getPlatform.AromaUnitSignalBinarySet |
Man page
|
| getPlatform.AromaUnitTypesFile |
Man page
|
| getPlatform.TextUnitNamesFile |
Man page
|
| getPlatform.UnitAnnotationDataFile |
Man page
|
| getPloidy |
Man page
|
| getPloidy.AromaMicroarrayDataFile |
Man page
|
| getPositions |
Man page
|
| getPositions.AromaUgpFile |
Man page
|
| getPositions.RawGenomicSignals |
Man page
|
| getProbeLength |
Man page
|
| getProbeLength.AromaCellSequenceFile |
Man page
|
| getProbePositionEffectDesignMatrix |
Man page
|
| getProbePositionEffectDesignMatrix.character |
Man page
|
| getProbePositionEffectDesignMatrix.raw |
Man page
|
| getRam |
Man page
|
| getRam.AromaSettings |
Man page
|
| getRandomSeed |
Man page
|
| getRandomSeed.CbsModel |
Man page
|
| getRawCnData |
Man page
|
| getRawCnData.CopyNumberChromosomalModel |
Man page
|
| getRefSetTuple |
Man page
|
| getRefSetTuple.CopyNumberChromosomalModel |
Man page
|
| getReference |
Man page
|
| getReference.CopyNumberChromosomalModel |
Man page
|
| getReferenceName |
Man page
|
| getReferenceName.SegmentationDataFile |
Man page
|
| getReferenceNames |
Man page
|
| getReferenceNames.SegmentationDataSet |
Man page
|
| getReferenceSetTuple |
Man page
|
| getReferenceSetTuple.CopyNumberChromosomalModel |
Man page
|
| getRegions |
Man page
|
| getRegions.CopyNumberSegmentationModel |
Man page
|
| getReportPath |
Man page
|
| getReportPath.ChromosomalModel |
Man page
|
| getReportPathPattern |
Man page
|
| getReportPathPattern.Explorer |
Man page
|
| getRootName |
Man page
|
| getRootName.AromaTabularBinaryFile |
Man page
|
| getRootName.AromaTabularBinarySet |
Man page
|
| getRootPath |
Man page
|
| getRootPath,AromaTransform-method |
Man page
|
| getRootPath,Explorer-method |
Man page
|
| getRootPath.AromaTransform |
Man page
|
| getRootPath.ChromosomalModel |
Man page
|
| getRootPath.Explorer |
Man page
|
| getSNPFields |
Man page
|
| getSNPFields.AbstractPSCNData |
Man page
|
| getSampleLabels |
Man page
|
| getSampleLabels.ChromosomeExplorer |
Man page
|
| getSampleLayerName |
Man page
|
| getSampleLayerName.Explorer |
Man page
|
| getSampleLayerPrefix |
Man page
|
| getSampleLayerPrefix.Explorer |
Man page
|
| getSampleName |
Man page
|
| getSampleName.SegmentationDataFile |
Man page
|
| getSampleNames |
Man page
|
| getSampleNames.SegmentationDataSet |
Man page
|
| getSetTag |
Man page
|
| getSetTag.ChromosomalModel |
Man page
|
| getSetTag.RawCopyNumberModel |
Man page
|
| getSetTuple |
Man page
|
| getSetTuple.ChromosomalModel |
Man page
|
| getSets.AromaMicroarrayDataSetTuple |
Man page
|
| getSets.ChromosomalModel |
Man page
|
| getSigma |
Man page
|
| getSigma.RawGenomicSignals |
Man page
|
| getSignalColumnName |
Man page
|
| getSignalColumnName.RawGenomicSignals |
Man page
|
| getSignalColumnNames |
Man page
|
| getSignalColumnNames.NonPairedPSCNData |
Man page
|
| getSignalColumnNames.PairedPSCNData |
Man page
|
| getSignalColumnNames.RawGenomicSignals |
Man page
|
| getSignals |
Man page
|
| getSignals.RawCopyNumbers |
Man page
|
| getSignals.RawGenomicSignals |
Man page
|
| getSnpNucleotides |
Man page
|
| getSnpNucleotides.AromaCellSequenceFile |
Man page
|
| getSnpPositions |
Man page
|
| getSnpPositions.AromaCellSequenceFile |
Man page
|
| getSnpShifts |
Man page
|
| getSnpShifts.AromaCellSequenceFile |
Man page
|
| getStateColorMap |
Man page
|
| getStateColorMap.SegmentedGenomicSignalsInterface |
Man page
|
| getStateColors |
Man page
|
| getStateColors.SegmentedGenomicSignalsInterface |
Man page
|
| getStates |
Man page
|
| getStates.SegmentedGenomicSignalsInterface |
Man page
|
| getSubname |
Man page
|
| getSubname.Explorer |
Man page
|
| getTCNs |
Man page
|
| getTCNs.PairedPSCNData |
Man page
|
| getTableOfArrays |
Man page
|
| getTableOfArrays.AromaMicroarrayDataSetTuple |
Man page
|
| getTableOfArrays.ChromosomalModel |
Man page
|
| getTags,AromaTransform-method |
Man page
|
| getTags,Explorer-method |
Man page
|
| getTags.Arguments |
Man page
|
| getTags.AromaMicroarrayDataSetTuple |
Man page
|
| getTags.AromaTransform |
Man page
|
| getTags.ChromosomalModel |
Man page
|
| getTags.CopyNumberSegmentationModel |
Man page
|
| getTags.Explorer |
Man page
|
| getTags.RichDataFrame |
Man page
|
| getTagsOfInput |
Man page
|
| getTagsOfInput.ChromosomeExplorer |
Man page
|
| getTagsOfInput.Explorer |
Man page
|
| getTemplatePath |
Man page
|
| getTemplatePath.Explorer |
Man page
|
| getTotalCopyNumbers |
Man page
|
| getTotalCopyNumbers.PairedPSCNData |
Man page
|
| getUniqueStates |
Man page
|
| getUniqueStates.SegmentedGenomicSignalsInterface |
Man page
|
| getUnitAnnotationDataFile |
Man page
|
| getUnitAnnotationDataFile,AromaPlatformInterface-method |
Man page
|
| getUnitAnnotationDataFile.AromaPlatformInterface |
Man page
|
| getUnitNames |
Man page
|
| getUnitNames.TextUnitNamesFile |
Man page
|
| getUnitNames.UnitNamesFile |
Man page
|
| getUnitNamesFile |
Man page
|
| getUnitNamesFile,AromaPlatformInterface-method |
Man page
|
| getUnitNamesFile.AromaPlatform |
Man page
|
| getUnitNamesFile.AromaPlatformInterface |
Man page
|
| getUnitNamesFile.AromaUnitTotalCnBinarySet |
Man page
|
| getUnitTypes |
Man page
|
| getUnitTypes.AromaUnitTypesFile |
Man page
|
| getUnitTypes.UnitTypesFile |
Man page
|
| getUnitTypesFile |
Man page
|
| getUnitTypesFile,AromaPlatformInterface-method |
Man page
|
| getUnitTypesFile.AromaPlatform |
Man page
|
| getUnitTypesFile.AromaPlatformInterface |
Man page
|
| getUnitsAt |
Man page
|
| getUnitsAt.AromaUgpFile |
Man page
|
| getUnitsOnChromosome |
Man page
|
| getUnitsOnChromosome.AromaUgpFile |
Man page
|
| getUnitsOnChromosome.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getUnitsOnChromosomes |
Man page
|
| getUnitsOnChromosomes.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| getUrlPath |
Man page
|
| getUrlPath.AromaRepository |
Man page
|
| getValueAt |
Man page
|
| getValueAt.CopyNumberRegions |
Man page
|
| getVerbose.AromaRepository |
Man page
|
| getVerbose.AromaSettings |
Man page
|
| getVersion.Explorer |
Man page
|
| getVirtualColumn |
Man page
|
| getVirtualColumn.RichDataFrame |
Man page
|
| getVirtualColumnFunction |
Man page
|
| getVirtualColumnFunction.RichDataFrame |
Man page
|
| getVirtualColumnFunctions |
Man page
|
| getVirtualColumnFunctions.RichDataFrame |
Man page
|
| getVirtualColumnNames |
Man page
|
| getVirtualColumnNames.RichDataFrame |
Man page
|
| getVirtualField |
Man page
|
| getVirtualField.SegmentedGenomicSignalsInterface |
Man page
|
| getVirtualLocusFields |
Man page
|
| getVirtualLocusFields.RawGenomicSignals |
Man page
|
| getVirtualLocusFields.SegmentedGenomicSignalsInterface |
Man page
|
| getWeights |
Man page
|
| getWeights.RawGenomicSignals |
Man page
|
| getXAM |
Man page
|
| getXAM.AromaMicroarrayDataFile |
Man page
|
| getXAM.AromaUnitTotalCnBinaryFile |
Man page
|
| getXScale |
Man page
|
| getXScale.RawGenomicSignals |
Man page
|
| getXY |
Man page
|
| getXY.RawGenomicSignals |
Man page
|
| getYScale |
Man page
|
| getYScale.RawGenomicSignals |
Man page
|
| getZooms |
Man page
|
| getZooms.ChromosomeExplorer |
Man page
|
| groupBySnpNucleotides |
Man page
|
| groupBySnpNucleotides.AromaCellSequenceFile |
Man page
|
| hasAlleleBFractions |
Man page
|
| hasAlleleBFractions.AromaUnitPscnBinaryFile |
Man page
|
| hasAlleleBFractions.AromaUnitTotalCnBinaryFile |
Man page
|
| hasAlleleBFractions.CopyNumberDataFile |
Man page
|
| hasAlleleBFractions.CopyNumberDataSet |
Man page
|
| hasAlleleBFractions.CopyNumberDataSetTuple |
Man page
|
| hasAttributeXY |
Man page
|
| hasAttributeXY.AromaMicroarrayDataFile |
Man page
|
| hasColumn |
Man page
|
| hasColumn.RichDataFrame |
Man page
|
| hasColumns |
Man page
|
| hasColumns.RichDataFrame |
Man page
|
| hasKnownPositions |
Man page
|
| hasKnownPositions.AbstractCNData |
Man page
|
| hasStrandiness |
Man page
|
| hasStrandiness.AromaUnitPscnBinaryFile |
Man page
|
| hasStrandiness.AromaUnitTotalCnBinaryFile |
Man page
|
| hasStrandiness.CopyNumberDataFile |
Man page
|
| hasStrandiness.CopyNumberDataSet |
Man page
|
| hasStrandiness.CopyNumberDataSetTuple |
Man page
|
| hasTotalCopyNumberRatios |
Man page
|
| hasTotalCopyNumberRatios.AromaUnitPscnBinaryFile |
Man page
|
| hasVirtualColumn |
Man page
|
| hasVirtualColumn.RichDataFrame |
Man page
|
| hasVirtualColumns |
Man page
|
| hasVirtualColumns.RichDataFrame |
Man page
|
| hasWeights |
Man page
|
| hasWeights.RawGenomicSignals |
Man page
|
| importFrom |
Man page
|
| importFrom.AromaTabularBinaryFile |
Man page
|
| importFromGenericTabularFile |
Man page
|
| importFromGenericTabularFile.AromaUflFile |
Man page
|
| importFromGenericTabularFile.AromaUgpFile |
Man page
|
| importFromTable |
Man page
|
| importFromTable.FileMatrix |
Man page
|
| importFromUnitTypesFile |
Man page
|
| importFromUnitTypesFile.AromaUnitTypesFile |
Man page
|
| indexOf,UnitNamesFile-method |
Man page
|
| indexOf.AromaMicroarrayDataSetTuple |
Man page
|
| indexOf.ChromosomalModel |
Man page
|
| indexOf.ChromosomeExplorer |
Man page
|
| indexOf.UnitNamesFile |
Man page
|
| indexOfColumn |
Man page
|
| indexOfColumn.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| indexOfUnits |
Man page
|
| indexOfUnits.AromaUnitTabularBinaryFile |
Man page
|
| interleave |
Man page
|
| interleave.Image |
Man page
|
| interleave.RasterImage |
Man page
|
| isAverageFile |
Man page
|
| isAverageFile.AromaMicroarrayDataFile |
Man page
|
| isAverageFile.AromaUnitSignalBinaryFile |
Man page
|
| isCompatibleWith |
Man page
|
| isCompatibleWith,AromaPlatformInterface-method |
Man page
|
| isCompatibleWith.AromaPlatformInterface |
Man page
|
| isDone,AromaTransform-method |
Man page
|
| isDone.AromaTransform |
Man page
|
| isHeterozygote |
Man page
|
| isHeterozygote.AromaUnitGenotypeCallFile |
Man page
|
| isHeterozygous |
Man page
|
| isHeterozygous.AromaUnitGenotypeCallFile |
Man page
|
| isHomozygote |
Man page
|
| isHomozygote.AromaUnitGenotypeCallFile |
Man page
|
| isHomozygous |
Man page
|
| isHomozygous.AromaUnitGenotypeCallFile |
Man page
|
| isMissing |
Man page
|
| isMissing.AromaCellCpgFile |
Man page
|
| isMissing.AromaCellPositionFile |
Man page
|
| isMissing.AromaCellSequenceFile |
Man page
|
| isPaired |
Man page
|
| isPaired.CopyNumberChromosomalModel |
Man page
|
| kernelSmoothing |
Man page
|
| kernelSmoothing.RawGenomicSignals |
Man page
|
| kernelSmoothing.numeric |
Man page
|
| kernelSmoothingByState |
Man page
|
| kernelSmoothingByState.SegmentedGenomicSignalsInterface |
Man page
|
| lapply |
Man page
|
| lapplyInChunks |
Man page
|
| lapplyInChunks.numeric |
Man page
|
| length.RichDataFrame |
Man page
|
| library |
Man page
Source code
|
| lines.CopyNumberOutliers |
Man page
|
| lines.CopyNumberRegions |
Man page
|
| lines.RawGenomicSignals |
Man page
|
| listFiles |
Man page
|
| listFiles,AromaRepository-method |
Man page
|
| listFiles.AromaRepository |
Man page
|
| listToXml |
Man page
|
| listToXml.list |
Man page
|
| loadAll |
Man page
|
| loadAll.SampleAnnotationSet |
Man page
|
| loadFit |
Man page
|
| loadFit.CbsSegmentationDataFile |
Man page
|
| loadFit.SegmentationDataFile |
Man page
|
| locallyUnique |
Man page
|
| locallyUnique.default |
Man page
|
| log2abs |
Man page
Source code
|
| log2center |
Man page
Source code
|
| log2neg |
Man page
Source code
|
| log2pos |
Man page
Source code
|
| matchPatterns |
Man page
|
| matchPatterns.SampleAnnotationFile |
Man page
|
| matrixBlockPolish |
Man page
|
| matrixBlockPolish.matrix |
Man page
|
| mergeBoxplotStats |
Man page
|
| mergeBoxplotStats.list |
Man page
|
| multiplyBy |
Man page
|
| multiplyBy.RawGenomicSignals |
Man page
|
| names.RichDataFrame |
Man page
|
| nbrOfArrays |
Man page
|
| nbrOfArrays,ChromosomalModel-method |
Man page
|
| nbrOfArrays,Explorer-method |
Man page
|
| nbrOfArrays.ChromosomalModel |
Man page
|
| nbrOfArrays.Explorer |
Man page
|
| nbrOfCells |
Man page
|
| nbrOfCells.AromaCellTabularBinaryFile |
Man page
|
| nbrOfChipTypes |
Man page
|
| nbrOfChipTypes,AromaMicroarrayDataSetTuple-method |
Man page
|
| nbrOfChipTypes,ChromosomalModel-method |
Man page
|
| nbrOfChipTypes.AromaMicroarrayDataSetTuple |
Man page
|
| nbrOfChipTypes.ChromosomalModel |
Man page
|
| nbrOfChromosomes |
Man page
|
| nbrOfChromosomes.CopyNumberRegions |
Man page
|
| nbrOfChromosomes.RawGenomicSignals |
Man page
|
| nbrOfColumns.AromaTabularBinaryFile |
Man page
|
| nbrOfEnzymes |
Man page
|
| nbrOfEnzymes.AromaUflFile |
Man page
|
| nbrOfLoci |
Man page
|
| nbrOfLoci.RawGenomicSignals |
Man page
|
| nbrOfReads |
Man page
|
| nbrOfReads.RawSequenceReads |
Man page
|
| nbrOfRegions |
Man page
|
| nbrOfRegions.CopyNumberOutliers |
Man page
|
| nbrOfRegions.CopyNumberRegions |
Man page
|
| nbrOfRows.AromaTabularBinaryFile |
Man page
|
| nbrOfUnits |
Man page
|
| nbrOfUnits.AromaUnitSignalBinaryFile |
Man page
|
| nbrOfUnits.AromaUnitTabularBinaryFile |
Man page
|
| nbrOfUnits.TextUnitNamesFile |
Man page
|
| nbrOfUnits.UnitAnnotationDataFile |
Man page
|
| nbrOfUnits.UnitNamesFile |
Man page
|
| nbrOfUnits.UnitTypesFile |
Man page
|
| newInstance.RawGenomicSignals |
Man page
|
| newInstance.RichDataFrame |
Man page
|
| newPlot |
Man page
|
| newPlot.CopyNumberChromosomalModel |
Man page
|
| norm2d |
Man page
|
| norm2d.matrix |
Man page
|
| normalizeGenotypeCone |
Man page
|
| normalizeGenotypeCone.matrix |
Man page
|
| normalizeTumorBoost |
Man page
|
| normalizeTumorBoost.PairedPSCNData |
Man page
|
| onFitAddGenotypeCalls |
Man page
|
| onFitAddGenotypeCalls.GladModel |
Man page
|
| onFitAddGenotypeCalls.default |
Man page
|
| orderAlongGenome |
Man page
|
| orderAlongGenome.AbstractCNData |
Man page
|
| plot.BinnedScatter |
Man page
|
| plot.CopyNumberSegmentationModel |
Man page
|
| plot.ProbePositionEffects |
Man page
|
| plot.RawAlleleBFractions |
Man page
|
| plot.RawCopyNumbers |
Man page
|
| plot.RawGenomicSignals |
Man page
|
| plot.RawMirroredAlleleBFractions |
Man page
|
| plot.RawSequenceReads |
Man page
|
| plot.SegmentedGenomicSignalsInterface |
Man page
|
| plotAxesLayers |
Man page
|
| plotAxesLayers.CopyNumberChromosomalModel |
Man page
|
| plotChromosomesLayers |
Man page
|
| plotChromosomesLayers.CopyNumberChromosomalModel |
Man page
|
| plotCopyNumberRegionLayers |
Man page
|
| plotCopyNumberRegionLayers.CopyNumberSegmentationModel |
Man page
|
| plotCoverageMap |
Man page
|
| plotCoverageMap.AromaUgpFile |
Man page
|
| plotCytobandLayers |
Man page
|
| plotCytobandLayers.CopyNumberChromosomalModel |
Man page
|
| plotFitLayers |
Man page
|
| plotFitLayers.CopyNumberChromosomalModel |
Man page
|
| plotGridHorizontalLayers |
Man page
|
| plotGridHorizontalLayers.CopyNumberChromosomalModel |
Man page
|
| plotProfile2 |
Man page
|
| plotProfile2.profileCGH |
Man page
|
| plotRawCNs |
Man page
|
| plotRawCNs.profileCGH |
Man page
|
| plotRawCopyNumbers |
Man page
|
| plotRawCopyNumbers.CopyNumberChromosomalModel |
Man page
|
| plotSampleLayers |
Man page
|
| plotSampleLayers.CopyNumberChromosomalModel |
Man page
|
| plotTracks |
Man page
|
| plotTracks,PairedPSCNData-method |
Man page
|
| plotTracks.PairedPSCNData |
Man page
|
| points.BinnedScatter |
Man page
|
| points.RawGenomicSignals |
Man page
|
| points.SegmentedGenomicSignalsInterface |
Man page
|
| pointsRawCNs |
Man page
|
| pointsRawCNs.default |
Man page
|
| pointsRawCNs.profileCGH |
Man page
|
| pointsSequence |
Man page
|
| pointsSequence.ProbePositionEffects |
Man page
|
| predict.ProbePositionEffects |
Man page
|
| print.RawGenomicSignals |
Man page
|
| print.RichDataFrame |
Man page
|
| process |
Man page
|
| process,AromaTransform-method |
Man page
|
| process,ChromosomeExplorer-method |
Man page
|
| process,Explorer-method |
Man page
|
| process.AromaTransform |
Man page
|
| process.ChromosomeExplorer |
Man page
|
| process.Explorer |
Man page
|
| processTime |
Man page
|
| processTime.default |
Man page
|
| prune |
Man page
|
| prune.CopyNumberRegions |
Man page
|
| rbind.RichDataFrame |
Man page
|
| read |
Man page
|
| read.RasterImage |
Man page
|
| readColumns.AromaTabularBinaryFile |
Man page
|
| readCpgs |
Man page
|
| readCpgs.AromaCellCpgFile |
Man page
|
| readDataFrame.AromaGenomeTextFile |
Man page
|
| readDataFrame.AromaTabularBinaryFile |
Man page
|
| readDataFrame.AromaUcscGenomeTextFile |
Man page
|
| readDataFrame.AromaUflFile |
Man page
|
| readDataFrame.AromaUnitChromosomeTabularBinaryFile |
Man page
|
| readDataFrame.AromaUnitSignalBinaryFile |
Man page
|
| readDataFrame.SampleAnnotationFile |
Man page
|
| readFooter |
Man page
|
| readFooter,AromaTabularBinaryFile-method |
Man page
|
| readFooter.AromaTabularBinaryFile |
Man page
|
| readHeader |
Man page
|
| readHeader.AromaTabularBinaryFile |
Man page
|
| readNeighborSequenceMatrix |
Man page
|
| readNeighborSequenceMatrix.AromaCellSequenceFile |
Man page
|
| readPairSequenceMatrix |
Man page
|
| readPairSequenceMatrix.AromaCellSequenceFile |
Man page
|
| readPositions |
Man page
|
| readPositions.AromaCellPositionFile |
Man page
|
| readRawFooter |
Man page
|
| readRawFooter.AromaTabularBinaryFile |
Man page
|
| readSequenceMatrix |
Man page
|
| readSequenceMatrix.AromaCellSequenceFile |
Man page
|
| readSequences |
Man page
|
| readSequences.AromaCellSequenceFile |
Man page
|
| readTargetStrands |
Man page
|
| readTargetStrands.AromaCellSequenceFile |
Man page
|
| remap |
Man page
|
| remap.default |
Man page
|
| reorder.BinnedScatter |
Man page
|
| require |
Man page
Source code
|
| requireWithMemory |
Man page
|
| requireWithMemory.default |
Man page
|
| rescale |
Man page
|
| rescale.Image |
Man page
|
| rescale.RasterImage |
Man page
|
| rgbTransform |
Man page
|
| rgbTransform.Image |
Man page
|
| save.RasterImage |
Man page
|
| segmentByCBS |
Man page
|
| segmentByCBS,RawGenomicSignals-method |
Man page
|
| segmentByCBS.NonPairedPSCNData |
Man page
|
| segmentByCBS.PairedPSCNData |
Man page
|
| segmentByCBS.RawGenomicSignals |
Man page
|
| segmentByGLAD |
Man page
|
| segmentByGLAD,RawGenomicSignals-method |
Man page
|
| segmentByGLAD.RawGenomicSignals |
Man page
|
| segmentByHaarSeg |
Man page
|
| segmentByHaarSeg,RawGenomicSignals-method |
Man page
|
| segmentByHaarSeg.RawGenomicSignals |
Man page
|
| segmentByMPCBS |
Man page
|
| segmentByMPCBS,RawGenomicSignals-method |
Man page
|
| segmentByMPCBS.RawGenomicSignals |
Man page
|
| segmentByPairedPSCBS |
Man page
|
| segmentByPairedPSCBS.PairedPSCNData |
Man page
|
| setAlias |
Man page
|
| setAlias,Explorer-method |
Man page
|
| setAlias.ChromosomalModel |
Man page
|
| setAlias.Explorer |
Man page
|
| setArrays |
Man page
|
| setArrays,ChromosomeExplorer-method |
Man page
|
| setArrays,Explorer-method |
Man page
|
| setArrays.ChromosomeExplorer |
Man page
|
| setArrays.Explorer |
Man page
|
| setAttributeXY |
Man page
|
| setAttributeXY.AromaMicroarrayDataFile |
Man page
|
| setAttributes.RichDataFrame |
Man page
|
| setAttributesBy.AromaMicroarrayDataSet |
Man page
|
| setAttributesBy.AromaTabularBinarySet |
Man page
|
| setAttributesBySampleAnnotationFile |
Man page
|
| setAttributesBySampleAnnotationFile.AromaMicroarrayDataSet |
Man page
|
| setAttributesBySampleAnnotationFile.AromaTabularBinarySet |
Man page
|
| setAttributesBySampleAnnotationSet |
Man page
|
| setAttributesBySampleAnnotationSet.AromaMicroarrayDataSet |
Man page
|
| setAttributesBySampleAnnotationSet.AromaTabularBinarySet |
Man page
|
| setAttributesByTags.AromaMicroarrayDataFile |
Man page
|
| setAttributesByTags.AromaTabularBinaryFile |
Man page
|
| setAttributesByTags.AromaTabularBinarySet |
Man page
|
| setBasicField |
Man page
|
| setBasicField.RawGenomicSignals |
Man page
|
| setChipType |
Man page
|
| setChipType.AbstractCNData |
Man page
|
| setChromosomes |
Man page
|
| setChromosomes.ChromosomalModel |
Man page
|
| setColumnNamesMap |
Man page
|
| setColumnNamesMap.RichDataFrame |
Man page
|
| setColumnNamesTranslator |
Man page
|
| setColumnNamesTranslator.RichDataFrame |
Man page
|
| setCytoband |
Man page
|
| setCytoband.ChromosomeExplorer |
Man page
|
| setGenome |
Man page
|
| setGenome.ChromosomalModel |
Man page
|
| setImageData |
Man page
|
| setImageData.Image |
Man page
|
| setImageData.RasterImage |
Man page
|
| setLocusFields |
Man page
|
| setLocusFields.RawGenomicSignals |
Man page
|
| setName.RawGenomicSignals |
Man page
|
| setName.RichDataFrame |
Man page
|
| setParallelSafe |
Man page
|
| setParallelSafe.Explorer |
Man page
|
| setPlatform |
Man page
|
| setPlatform.AbstractCNData |
Man page
|
| setRam |
Man page
|
| setRam.AromaSettings |
Man page
|
| setRandomSeed |
Man page
|
| setRandomSeed.CbsModel |
Man page
|
| setReference |
Man page
|
| setReference.CopyNumberChromosomalModel |
Man page
|
| setReportPathPattern |
Man page
|
| setReportPathPattern.Explorer |
Man page
|
| setSigma |
Man page
|
| setSigma.RawGenomicSignals |
Man page
|
| setSignals |
Man page
|
| setSignals.RawGenomicSignals |
Man page
|
| setStateColorMap |
Man page
|
| setStateColorMap.SegmentedGenomicSignalsInterface |
Man page
|
| setStates |
Man page
|
| setStates.SegmentedGenomicSignalsInterface |
Man page
|
| setSubname |
Man page
|
| setSubname.Explorer |
Man page
|
| setTags.AromaTransform |
Man page
|
| setTags.RichDataFrame |
Man page
|
| setVerbose |
Man page
|
| setVerbose.AromaRepository |
Man page
|
| setVerbose.AromaSettings |
Man page
|
| setVirtualColumn |
Man page
|
| setVirtualColumn.RichDataFrame |
Man page
|
| setVirtualColumnFunctions |
Man page
|
| setVirtualColumnFunctions.RichDataFrame |
Man page
|
| setWeights |
Man page
|
| setWeights.RawGenomicSignals |
Man page
|
| setXScale |
Man page
|
| setXScale.RawGenomicSignals |
Man page
|
| setYScale |
Man page
|
| setYScale.RawGenomicSignals |
Man page
|
| setZooms |
Man page
|
| setZooms.ChromosomeExplorer |
Man page
|
| setup |
Man page
|
| setup.ChromosomeExplorer |
Man page
|
| setup.Explorer |
Man page
|
| shakyText |
Man page
|
| shakyText.default |
Man page
|
| signalRange |
Man page
|
| signalRange.RawGenomicSignals |
Man page
|
| simulateRawCopyNumbers |
Man page
|
| simulateRawCopyNumbers.CopyNumberRegions |
Man page
|
| smoothWRMA |
Man page
|
| smoothWRMA.matrix |
Man page
|
| smoothWSA |
Man page
|
| smoothWSA.matrix |
Man page
|
| sort.RawGenomicSignals |
Man page
|
| splitByReportPathPattern |
Man page
|
| splitByReportPathPattern.Explorer |
Man page
|
| splitInChunks |
Man page
|
| splitInChunks.numeric |
Man page
|
| sqrtabs |
Man page
Source code
|
| sqrtcenter |
Man page
Source code
|
| sqrtneg |
Man page
Source code
|
| sqrtpos |
Man page
Source code
|
| sqrtsign |
Man page
Source code
|
| stextChipType |
Man page
|
| stextChipType.character |
Man page
|
| stextLabel |
Man page
|
| stextLabel.AromaMicroarrayDataFile |
Man page
|
| stextLabels |
Man page
|
| stextLabels.AromaMicroarrayDataFile |
Man page
|
| stextSize |
Man page
|
| stextSize.AromaMicroarrayDataFile |
Man page
|
| str.RasterImage |
Man page
|
| stringTree |
Man page
|
| stringTree.character |
Man page
|
| subsample |
Man page
|
| subsample.BinnedScatter |
Man page
|
| subset.AromaTabularBinaryFile |
Man page
|
| subset.BinnedScatter |
Man page
|
| subset.CopyNumberRegions |
Man page
|
| subset.RichDataFrame |
Man page
|
| subtractBy |
Man page
|
| subtractBy.RawGenomicSignals |
Man page
|
| summary.AromaTabularBinaryFile |
Man page
|
| summary.RawGenomicSignals |
Man page
|
| summaryOfUnits |
Man page
|
| summaryOfUnits.AromaUflFile |
Man page
|
| text.ProbePositionEffects |
Man page
|
| textSequence |
Man page
|
| textSequence.ProbePositionEffects |
Man page
|
| translateColumnNames.RichDataFrame |
Man page
|
| unique.CopyNumberRegions |
Man page
|
| updateCpgs |
Man page
|
| updateCpgs.AromaCellCpgFile |
Man page
|
| updateData |
Man page
|
| updateData.AromaTabularBinaryFile |
Man page
|
| updateDataColumn |
Man page
|
| updateDataColumn.AromaTabularBinaryFile |
Man page
|
| updateGenotypes |
Man page
|
| updateGenotypes.AromaUnitGenotypeCallFile |
Man page
|
| updatePositions |
Man page
|
| updatePositions.AromaCellPositionFile |
Man page
|
| updateSequenceMatrix |
Man page
|
| updateSequenceMatrix.AromaCellSequenceFile |
Man page
|
| updateSequences |
Man page
|
| updateSequences.AromaCellSequenceFile |
Man page
|
| updateSetupExplorerFile |
Man page
|
| updateSetupExplorerFile,ChromosomeExplorer-method |
Man page
|
| updateSetupExplorerFile.ChromosomeExplorer |
Man page
|
| updateSetupExplorerFile.Explorer |
Man page
|
| updateTargetStrands |
Man page
|
| updateTargetStrands.AromaCellSequenceFile |
Man page
|
| validate.AromaMicroarrayDataSet |
Man page
|
| validate.AromaUnitSignalBinarySet |
Man page
|
| weightedMean |
Man page
|
| whatDataType |
Man page
|
| whatDataType.default |
Man page
|
| write |
Man page
|
| write.RasterImage |
Man page
|
| write.default |
Man page
|
| writeAxesLayers |
Man page
|
| writeAxesLayers.ChromosomeExplorer |
Man page
|
| writeCopyNumberRegionLayers |
Man page
|
| writeCopyNumberRegionLayers.ChromosomeExplorer |
Man page
|
| writeCytobandLayers |
Man page
|
| writeCytobandLayers.ChromosomeExplorer |
Man page
|
| writeDataFrame |
Man page
|
| writeDataFrame,AromaUnitSignalBinaryFile-method |
Man page
|
| writeDataFrame,AromaUnitSignalBinarySet-method |
Man page
|
| writeDataFrame,AromaUnitTabularBinaryFile-method |
Man page
|
| writeDataFrame.AromaUnitFracBCnBinarySet |
Man page
|
| writeDataFrame.AromaUnitPscnBinarySet |
Man page
|
| writeDataFrame.AromaUnitSignalBinaryFile |
Man page
|
| writeDataFrame.AromaUnitSignalBinarySet |
Man page
|
| writeDataFrame.AromaUnitTabularBinaryFile |
Man page
|
| writeDataFrame.AromaUnitTotalCnBinarySet |
Man page
|
| writeFooter |
Man page
|
| writeFooter,AromaTabularBinaryFile-method |
Man page
|
| writeFooter.AromaTabularBinaryFile |
Man page
|
| writeGraphs |
Man page
|
| writeGraphs.ChromosomeExplorer |
Man page
|
| writeGridHorizontalLayers |
Man page
|
| writeGridHorizontalLayers.ChromosomeExplorer |
Man page
|
| writeImage |
Man page
|
| writeImage.Image |
Man page
|
| writeImage.RasterImage |
Man page
|
| writeRawCopyNumberLayers |
Man page
|
| writeRawCopyNumberLayers.ChromosomeExplorer |
Man page
|
| writeRawFooter |
Man page
|
| writeRawFooter.AromaTabularBinaryFile |
Man page
|
| writeRegions |
Man page
|
| writeRegions.ChromosomeExplorer |
Man page
|
| writeRegions.CopyNumberSegmentationModel |
Man page
|
| writeRegions.GladModel |
Man page
|
| xMax |
Man page
|
| xMax.CopyNumberRegions |
Man page
|
| xMax.RawGenomicSignals |
Man page
|
| xMin |
Man page
|
| xMin.CopyNumberRegions |
Man page
|
| xMin.RawGenomicSignals |
Man page
|
| xRange |
Man page
|
| xRange.CopyNumberRegions |
Man page
|
| xRange.RawGenomicSignals |
Man page
|
| xSeq |
Man page
|
| xSeq.RawGenomicSignals |
Man page
|
| xmlToList |
Man page
|
| xmlToList.character |
Man page
|
| yMax |
Man page
|
| yMax.RawGenomicSignals |
Man page
|
| yMin |
Man page
|
| yMin.RawGenomicSignals |
Man page
|
| yRange |
Man page
|
| yRange.RawGenomicSignals |
Man page
|
| yellow.colors |
Man page
Source code
|
