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install.packages('aroma.cn')
Monthly Downloads
806
Version
1.6.1
License
LGPL (>= 2.1)
Issues
4
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Repository
https://github.com/HenrikBengtsson/aroma.cn
Homepage
http://www.aroma-project.org/
Maintainer
Henrik Bengtsson
Last Published
October 27th, 2015
Functions in aroma.cn (1.6.1)
Search functions
aroma.cn-package
Package aroma.cn
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