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 |