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aroma.cn (version 0.9.2)
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
0.9.2
License
LGPL (>= 2.1)
Maintainer
Henrik Bengtsson
Last Published
November 3rd, 2011
Functions in aroma.cn (0.9.2)
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callAllelicBalanceByBAFs.PairedPSCBS
Calls regions that are in allelic balance
callCopyNeutralRegions.PairedPSCBS
Calls regions that are copy neutral
normalizeBAFsByRegions.PairedPSCBS
Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
testAllelicBalanceByBAFs
Tests for allelic balance in a genomic region
TumorBoostNormalization
The TumorBoostNormalization class
getInputDataSets.MultiSourceCopyNumberNormalization
Gets the list of data sets to be normalized
getSubsetToFit.MultiSourceCopyNumberNormalization
Gets subset of (smoothing) units for fitting the model
fitOne.MultiSourceCopyNumberNormalization
Fits the multi-source model for one sample
deShearC1C2.PairedPSCBS
Correct for shearing in (C1,C2) space based on region-based PSCN estimates
PrincipalCurveNormalization
The PrincipalCurveNormalization class
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
aroma.cn-package
Package aroma.cn
XYCurveNormalization
The XYCurveNormalization class
calibrateC1C2.PairedPSCBS
Calibrates ASCN signals in (C1,C2) space based on region-based PSCN estimates
getAllNames.MultiSourceCopyNumberNormalization
Gets the names of all unique samples across all sources
MultiSourceCopyNumberNormalization
The MultiSourceCopyNumberNormalization class
TotalCnSmoothing
The abstract TotalCnSmoothing class
AbstractCurveNormalization
The AbstractCurveNormalization class
TotalCnKernelSmoothing
The TotalCnKernelSmoothing class
callXXorXY.numeric
Calls XX or XY from ChrX allele B fractions of a normal sample
process.MultiSourceCopyNumberNormalization
Normalizes all samples
getFitAromaUgpFile.MultiSourceCopyNumberNormalization
Gets the UGP file specifying the common set of loci to normalize at
Non-documented objects
Non-documented objects
getSmoothedDataSets.MultiSourceCopyNumberNormalization
Gets the data sets smoothed toward the UGP file
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
Gets a list of data files for a particular name across several data sets
callPeaks.PeaksAndValleys
Calls the peaks in peaks-and-valley estimates
cnr
Simple creation of a CopyNumberRegions object
findAtomicAberrations.CopyNumberRegions
Finds all possible atomic regions