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aroma.cn (version 1.3.3)
Copy-number analysis of large microarray data sets
Description
Analysis of copy-number estimates obtained from various platforms.
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Install
install.packages('aroma.cn')
Monthly Downloads
524
Version
1.3.3
License
LGPL (>= 2.1)
Maintainer
Henrik Bengtsson
Last Published
April 22nd, 2013
Functions in aroma.cn (1.3.3)
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TotalCnSmoothing
The abstract TotalCnSmoothing class
MultiSourceCopyNumberNormalization
The MultiSourceCopyNumberNormalization class
normalizePrincipalCurve.matrix
Normalizes data in K dimensions using principal curves
PairedPscbsModel
The PairedPscbsModel class
Non-documented objects
Non-documented objects
TotalCnKernelSmoothing
The TotalCnKernelSmoothing class
getSmoothedDataSets.MultiSourceCopyNumberNormalization
Gets the data sets smoothed toward the UGP file
XYCurveNormalization
The XYCurveNormalization class
TumorBoostNormalization
The TumorBoostNormalization class
getSubsetToFit.MultiSourceCopyNumberNormalization
Gets subset of (smoothing) units for fitting the model
callCopyNeutralRegions.PairedPSCBS
Calls regions that are copy neutral
normalizeBAFsByRegions.PairedPSCBS
Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
deShearC1C2.PairedPSCBS
Correct for shearing in (C1,C2) space based on region-based PSCN estimates
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
Gets a list of data files for a particular name across several data sets
TotalCnBinnedSmoothing
The TotalCnBinnedSmoothing class
findAtomicAberrations.CopyNumberRegions
Finds all possible atomic regions
PrincipalCurveNormalization
The PrincipalCurveNormalization class
getFitAromaUgpFile.MultiSourceCopyNumberNormalization
Gets the UGP file specifying the common set of loci to normalize at
getAllNames.MultiSourceCopyNumberNormalization
Gets the names of all unique samples across all sources
callPeaks.PeaksAndValleys
Calls the peaks in peaks-and-valley estimates
aroma.cn-package
Package aroma.cn
testAllelicBalanceByBAFs
Tests for allelic balance in a genomic region
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
callAllelicBalanceByBAFs.PairedPSCBS
Calls regions that are in allelic balance
callXXorXY.numeric
Calls XX or XY from ChrX allele B fractions of a normal sample
cnr
Simple creation of a CopyNumberRegions object
normalizeMirroredBAFsByRegions.matrix
Normalizes region-level mirrored allele B fractions (mBAFs)
getInputDataSets.MultiSourceCopyNumberNormalization
Gets the list of data sets to be normalized
AbstractCurveNormalization
The AbstractCurveNormalization class
process.MultiSourceCopyNumberNormalization
Normalizes all samples