Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

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Documentation for package ‘aroma.core’ version 3.3.0

• DESCRIPTION file.

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aroma.core-package	Package aroma.core
AbstractCNData	The AbstractCNData class
AbstractPSCNData	The AbstractPSCNData class
aroma.core	Package aroma.core
AromaCellCpgFile	A binary file holding local CpG density for each cell (probe/feature)
AromaCellPositionFile	A binary file holding chromosome/position for each cell
AromaCellTabularBinaryFile	The AromaCellTabularBinaryFile class
AromaGenomeTextFile	The AromaGenomeTextFile class
AromaMicroarrayDataFile	The abstract AromaMicroarrayDataFile class
AromaMicroarrayDataSet	The AromaMicroarrayDataSet class
AromaMicroarrayDataSetTuple	The AromaMicroarrayDataSetTuple class
AromaMicroarrayTabularBinaryFile	The AromaMicroarrayTabularBinaryFile class
AromaPlatform	The AromaPlatform class
AromaPlatformInterface	The AromaPlatformInterface class
AromaRepository	The AromaRepository class
AromaTabularBinaryFile	The AromaTabularBinaryFile class
AromaTabularBinarySet	The AromaTabularBinarySet class
AromaTransform	The AromaTransform class
AromaUnitCallFile	The AromaUnitCallFile class
AromaUnitCallSet	The AromaUnitCallSet class
AromaUnitFracBCnBinaryFile	The AromaUnitFracBCnBinaryFile class
AromaUnitFracBCnBinarySet	The AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFile	The AromaUnitGenotypeCallFile class
AromaUnitGenotypeCallSet	The AromaUnitGenotypeCallSet class
AromaUnitPscnBinaryFile	The AromaUnitPscnBinaryFile class
AromaUnitPscnBinarySet	The AromaUnitPscnBinarySet class
AromaUnitSignalBinaryFile	The AromaUnitSignalBinaryFile class
AromaUnitSignalBinarySet	The AromaUnitSignalBinarySet class
AromaUnitTabularBinaryFile	The AromaUnitTabularBinaryFile class
AromaUnitTotalCnBinaryFile	The AromaUnitTotalCnBinaryFile class
AromaUnitTotalCnBinarySet	The AromaUnitTotalCnBinarySet class
AromaUnitTypesFile	The AromaUnitTypesFile class
BinnedScatter	The BinnedScatter class
binnedSmoothing	Binned smoothing of a matrix column by column
binnedSmoothing.numeric	Binned smoothing of a matrix column by column
CbsModel	The CbsModel class
ChromosomalModel	The ChromosomalModel class
ChromosomeExplorer	The ChromosomeExplorer class
colBinnedSmoothing	Binned smoothing of a matrix column by column
colBinnedSmoothing.matrix	Binned smoothing of a matrix column by column
colKernelSmoothing	Kernel smoothing of a matrix column by column
colKernelSmoothing.matrix	Kernel smoothing of a matrix column by column
CopyNumberChromosomalModel	The CopyNumberChromosomalModel class
CopyNumberSegmentationModel	The CopyNumberSegmentationModel class
doCBS	Performs Circular Binary Segmentation (CBS) on a data set
doCBS.character	Performs Circular Binary Segmentation (CBS) on a data set
doCBS.CopyNumberDataSet	Performs Circular Binary Segmentation (CBS) on a data set
doCBS.CopyNumberDataSetTuple	Performs Circular Binary Segmentation (CBS) on a data set
doCBS.default	Performs Circular Binary Segmentation (CBS) on a data set
Explorer	The Explorer class
GladModel	The GladModel class
HaarSegModel	The HaarSegModel class
kernelSmoothing	Kernel smoothing of a matrix column by column
kernelSmoothing.numeric	Kernel smoothing of a matrix column by column
NonPairedPSCNData	The NonPairedPSCNData class
PairedPSCNData	The PairedPSCNData class
ParametersInterface	The ParametersInterface class interface
RawAlleleBFractions	The RawAlleleBFractions class
RawCopyNumberModel	The RawCopyNumberModel class
RawCopyNumbers	The RawCopyNumbers class
RawGenomicSignals	The RawGenomicSignals class
RawMirroredAlleleBFractions	The RawMirroredAlleleBFractions class
RawSequenceReads	The RawSequenceReads class
SegmentedAlleleBFractions	The SegmentedAlleleBFractions class
SegmentedCopyNumbers	The SegmentedCopyNumbers class
SegmentedGenomicSignalsInterface	The SegmentedGenomicSignalsInterface class interface
UnitAnnotationDataFile	The UnitAnnotationDataFile interface class
UnitNamesFile	The UnitNamesFile interface class
UnitTypesFile	The UnitTypesFile interface class