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