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aroma.cn (version 1.0.0)
Copy-number analysis of large microarray data sets
Description
Package for analysis of copy-number estimates obtained from various platforms.
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Install
install.packages('aroma.cn')
Monthly Downloads
492
Version
1.0.0
License
LGPL (>= 2.1)
Maintainer
Henrik Bengtsson
Last Published
January 12th, 2012
Functions in aroma.cn (1.0.0)
Search functions
callCopyNeutralRegions.PairedPSCBS
Calls regions that are copy neutral
callPeaks.PeaksAndValleys
Calls the peaks in peaks-and-valley estimates
Non-documented objects
Non-documented objects
findAtomicAberrations.CopyNumberRegions
Finds all possible atomic regions
process.MultiSourceCopyNumberNormalization
Normalizes all samples
TotalCnKernelSmoothing
The TotalCnKernelSmoothing class
TotalCnSmoothing
The abstract TotalCnSmoothing class
aroma.cn-package
Package aroma.cn
normalizeMirroredBAFsByRegions.matrix
Normalizes region-level mirrored allele B fractions (mBAFs)
findNeutralCopyNumberState
Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates
MultiSourceCopyNumberNormalization
The MultiSourceCopyNumberNormalization class
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
Gets a list of data files for a particular name across several data sets
PrincipalCurveNormalization
The PrincipalCurveNormalization class
getInputDataSets.MultiSourceCopyNumberNormalization
Gets the list of data sets to be normalized
normalizeBAFsByRegions.PairedPSCBS
Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
TumorBoostNormalization
The TumorBoostNormalization class
callXXorXY.numeric
Calls XX or XY from ChrX allele B fractions of a normal sample
cnr
Simple creation of a CopyNumberRegions object
getFitAromaUgpFile.MultiSourceCopyNumberNormalization
Gets the UGP file specifying the common set of loci to normalize at
AbstractCurveNormalization
The AbstractCurveNormalization class
calibrateC1C2.PairedPSCBS
Calibrates ASCN signals in (C1,C2) space based on region-based PSCN estimates
fitOne.MultiSourceCopyNumberNormalization
Fits the multi-source model for one sample
getSmoothedDataSets.MultiSourceCopyNumberNormalization
Gets the data sets smoothed toward the UGP file
deShearC1C2.PairedPSCBS
Correct for shearing in (C1,C2) space based on region-based PSCN estimates
getSubsetToFit.MultiSourceCopyNumberNormalization
Gets subset of (smoothing) units for fitting the model
XYCurveNormalization
The XYCurveNormalization class
callAllelicBalanceByBAFs.PairedPSCBS
Calls regions that are in allelic balance
getAllNames.MultiSourceCopyNumberNormalization
Gets the names of all unique samples across all sources
testAllelicBalanceByBAFs
Tests for allelic balance in a genomic region