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