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

AbstractCurveNormalizationThe AbstractCurveNormalization class
aroma.cn-packagePackage aroma.cn
callAllelicBalanceByBAFs.PairedPSCBSCalls regions that are in allelic balance
callCopyNeutralRegions.PairedPSCBSCalls regions that are copy neutral
callPeaks.PeaksAndValleysCalls the peaks in peaks-and-valley estimates
callXXorXY.numericCalls XX or XY from ChrX allele B fractions of a normal...
cnrSimple creation of a CopyNumberRegions object
extractTupleOfDataFiles.MultiSourceCopyNumberNormalizationGets a list of data files for a particular name across...
findAtomicAberrations.CopyNumberRegionsFinds all possible atomic regions
fitOne.MultiSourceCopyNumberNormalizationFits the multi-source model for one sample
getAllNames.MultiSourceCopyNumberNormalizationGets the names of all unique samples across all sources
getFitAromaUgpFile.MultiSourceCopyNumberNormalizationGets the UGP file specifying the common set of loci to...
getInputDataSets.MultiSourceCopyNumberNormalizationGets the list of data sets to be normalized
getSmoothedDataSets.MultiSourceCopyNumberNormalizationGets the data sets smoothed toward the UGP file
getSubsetToFit.MultiSourceCopyNumberNormalizationGets subset of (smoothing) units for fitting the model
MultiSourceCopyNumberNormalizationThe MultiSourceCopyNumberNormalization class
Non-documented_objectsNon-documented objects
normalizeBAFsByRegions.PairedPSCBSNormalizes allele B fractions (BAFs) based on region-based...
normalizeMirroredBAFsByRegions.matrixNormalizes region-level mirrored allele B fractions (mBAFs)
normalizePrincipalCurve.matrixNormalizes data in K dimensions using principal curves
PairedPscbsModelThe PairedPscbsModel class
PrincipalCurveNormalizationThe PrincipalCurveNormalization class
process.MultiSourceCopyNumberNormalizationNormalizes all samples
testAllelicBalanceByBAFsTests for allelic balance in a genomic region
TotalCnBinnedSmoothingThe TotalCnBinnedSmoothing class
TotalCnKernelSmoothingThe TotalCnKernelSmoothing class
TotalCnSmoothingThe abstract TotalCnSmoothing class
TumorBoostNormalizationThe TumorBoostNormalization class
XYCurveNormalizationThe XYCurveNormalization class
aroma.cn documentation built on May 29, 2017, 7:56 p.m.