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


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Documentation for package ‘aroma.core’ version 3.2.2

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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