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