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aroma.cn (version 0.8.1)

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

0.8.1

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

August 1st, 2011

Functions in aroma.cn (0.8.1)

findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
callXXorXY.numeric

Calls XX or XY from ChrX allele B fractions of a normal sample
Non-documented objects

Non-documented objects
calibrateC1C2.PairedPSCBS

Calibrates ASCN signals in (C1,C2) space based on region-based PSCN estimates
testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region
findNeutralCopyNumberState

Call segments to be copy neutral based on allelic imbalance calls and total copy number 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
getSubsetToFit.MultiSourceCopyNumberNormalization

Gets subset of (smoothing) units for fitting the model
aroma.cn-package

Package aroma.cn
cnr

Simple creation of a CopyNumberRegions object
PrincipalCurveNormalization

The PrincipalCurveNormalization class
getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file
XYCurveNormalization

The XYCurveNormalization class
callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
AbstractCurveNormalization

The AbstractCurveNormalization class
TotalCnSmoothing

The abstract TotalCnSmoothing class
normalizeMirroredBAFsByRegions.matrix

Normalizes region-level mirrored allele B fractions (mBAFs)
fitOne.MultiSourceCopyNumberNormalization

Fits the multi-source model for one sample
normalizeBAFsByRegions.PairedPSCBS

Normalizes allele B fractions (BAFs) based on region-based PSCN estimates
getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

Gets the UGP file specifying the common set of loci to normalize at
TumorBoostNormalization

The TumorBoostNormalization class
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral
process.MultiSourceCopyNumberNormalization

Normalizes all samples
getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources