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Copy-Number Analysis of Large Microarray Data Sets

Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.

Functions in

Name Description Package
callPeaks.PeaksAndValleys Calls the peaks in peaks-and-valley estimates
findAtomicAberrations.CopyNumberRegions Finds all possible atomic regions
callCopyNeutralRegions.PairedPSCBS Calls regions that are copy neutral
TumorBoostNormalization The TumorBoostNormalization class
TotalCnKernelSmoothing The TotalCnKernelSmoothing class
PrincipalCurveNormalization The PrincipalCurveNormalization class
TotalCnBinnedSmoothing The TotalCnBinnedSmoothing class
XYCurveNormalization The XYCurveNormalization class
fitOne.MultiSourceCopyNumberNormalization Fits the multi-source model for one sample
process.MultiSourceCopyNumberNormalization Normalizes all samples
callAllelicBalanceByBAFs.PairedPSCBS Calls regions that are in allelic balance
getAllNames.MultiSourceCopyNumberNormalization Gets the names of all unique samples across all sources
getSubsetToFit.MultiSourceCopyNumberNormalization Gets subset of (smoothing) units for fitting the model
normalizeBAFsByRegions.PairedPSCBS Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
normalizePrincipalCurve.matrix Normalizes data in K dimensions using principal curves
TotalCnSmoothing The abstract TotalCnSmoothing class
callXXorXY.numeric Calls XX or XY from ChrX allele B fractions of a normal sample
getSmoothedDataSets.MultiSourceCopyNumberNormalization Gets the data sets smoothed toward the UGP file
getInputDataSets.MultiSourceCopyNumberNormalization Gets the list of data sets to be normalized
testAllelicBalanceByBAFs Tests for allelic balance in a genomic region
normalizeMirroredBAFsByRegions.matrix Normalizes region-level mirrored allele B fractions (mBAFs)
Non-documented objects Non-documented objects
PairedPscbsModel The PairedPscbsModel class
MultiSourceCopyNumberNormalization The MultiSourceCopyNumberNormalization class
cnr Simple creation of a CopyNumberRegions object
AbstractCurveNormalization The AbstractCurveNormalization class
getFitAromaUgpFile.MultiSourceCopyNumberNormalization Gets the UGP file specifying the common set of loci to normalize at
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization Gets a list of data files for a particular name across several data sets
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SuggestsNote BioC (>= 3.0), Recommended: aroma.light, DNAcopy
Date 2015-10-27
License LGPL (>= 2.1)
LazyLoad TRUE
biocViews ProprietaryPlatforms, aCGH, CopyNumberVariants, SNP, Microarray, OneChannel, TwoChannel, DataImport, DataRepresentation, Preprocessing, QualityControl
NeedsCompilation no
Packaged 2015-10-27 19:42:18 UTC; hb
Repository CRAN
Date/Publication 2015-10-28 00:08:16

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