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