Man pages for aroma.cn
Copy-Number Analysis of Large Microarray Data Sets
| 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 |
