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aroma.cn (version 0.8.0)

Copy-number analysis of large microarray data sets

Description

Package for analysis of copy-number estimates obtained from various platforms.

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Version

Install

install.packages('aroma.cn')

Monthly Downloads

269

Version

0.8.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

July 23rd, 2011

Functions in aroma.cn (0.8.0)

fitOne.MultiSourceCopyNumberNormalization

Fits the multi-source model for one sample
process.MultiSourceCopyNumberNormalization

Normalizes all samples
AbstractCurveNormalization

The AbstractCurveNormalization class
getSubsetToFit.MultiSourceCopyNumberNormalization

Gets subset of (smoothing) units for fitting the model
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
cnr

Simple creation of a CopyNumberRegions object
deShearC1C2.PairedPSCBS

Correct for shearing in (C1,C2) space based on region-based PSCN estimates
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral
aroma.cn-package

Package aroma.cn
findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
normalizeBAFsByRegions.PairedPSCBS

Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
XYCurveNormalization

The XYCurveNormalization class
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization

Gets a list of data files for a particular name across several data sets
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

Gets the UGP file specifying the common set of loci to normalize at
callXXorXY.numeric

Calls XX or XY from ChrX allele B fractions of a normal sample
getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized
normalizeMirroredBAFsByRegions.matrix

Normalizes region-level mirrored allele B fractions (mBAFs)
TotalCnSmoothing

The abstract TotalCnSmoothing class
findNeutralCopyNumberState

Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates
Non-documented objects

Non-documented objects
PrincipalCurveNormalization

The PrincipalCurveNormalization class
callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file
testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region
TumorBoostNormalization

The TumorBoostNormalization 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