Package aroma.cn
deShearC1C2UNDERSCORE20120922.PairedPSCBS
Correct for shearing in (C1,C2) space based on region-based PSCN estimates
The abstract TotalCnSmoothing class
callAllelicBalanceByBAFs.PairedPSCBS
Calls regions that are in allelic balance
The TotalCnBinnedSmoothing class
normalizePrincipalCurve.matrix
Normalizes data in K dimensions using principal curves
The TotalCnKernelSmoothing class
PrincipalCurveNormalization
The PrincipalCurveNormalization class
getInputDataSets.MultiSourceCopyNumberNormalization
Gets the list of data sets to be normalized
getFitAromaUgpFile.MultiSourceCopyNumberNormalization
Gets the UGP file specifying the common set of loci to normalize at
The TumorBoostNormalization class
The PairedPscbsModel class
getSubsetToFit.MultiSourceCopyNumberNormalization
Gets subset of (smoothing) units for fitting the model
Tests for allelic balance in a genomic region
callPeaks.PeaksAndValleys
Calls the peaks in peaks-and-valley estimates
getAllNames.MultiSourceCopyNumberNormalization
Gets the names of all unique samples across all sources
The XYCurveNormalization class
getSmoothedDataSets.MultiSourceCopyNumberNormalization
Gets the data sets smoothed toward the UGP file
normalizeBAFsByRegions.PairedPSCBS
Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
fitOne.MultiSourceCopyNumberNormalization
Fits the multi-source model for one sample
callCopyNeutralRegions.PairedPSCBS
Calls regions that are copy neutral
process.MultiSourceCopyNumberNormalization
Normalizes all samples
normalizeMirroredBAFsByRegions.matrix
Normalizes region-level mirrored allele B fractions (mBAFs)
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
Gets a list of data files for a particular name across several data sets
Non-documented objects
MultiSourceCopyNumberNormalization
The MultiSourceCopyNumberNormalization class
findAtomicAberrations.CopyNumberRegions
Finds all possible atomic regions
Calls XX or XY from ChrX allele B fractions of a normal sample
calibrateC1C2.PairedPSCBS
Calibrates ASCN signals in (C1,C2) space based on region-based PSCN estimates
Simple creation of a CopyNumberRegions object
AbstractCurveNormalization
The AbstractCurveNormalization class