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aroma.cn (version 1.3.0)

Copy-number analysis of large microarray data sets

Description

Analysis of copy-number estimates obtained from various platforms.

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Version

Install

install.packages('aroma.cn')

Monthly Downloads

269

Version

1.3.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

January 8th, 2013

Functions in aroma.cn (1.3.0)

PrincipalCurveNormalization

The PrincipalCurveNormalization class

callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance

findNeutralCopyNumberState

Call segments to be copy neutral based on allelic imbalance calls and total copy number estimates

TumorBoostNormalization

The TumorBoostNormalization class

TotalCnBinnedSmoothing

The TotalCnBinnedSmoothing class

deShearC1C2.PairedPSCBS

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

callPeaks.PeaksAndValleys

Calls the peaks in peaks-and-valley estimates

XYCurveNormalization

The XYCurveNormalization class

getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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

callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral

AbstractCurveNormalization

The AbstractCurveNormalization class

getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized

testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region

normalizeBAFsByRegions.PairedPSCBS

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

fitOne.MultiSourceCopyNumberNormalization

Fits the multi-source model for one sample

MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class

Non-documented objects

calibrateC1C2.PairedPSCBS

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

aroma.cn-package

Package aroma.cn

cnr

Simple creation of a CopyNumberRegions object

getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources

normalizeMirroredBAFsByRegions.matrix

Normalizes region-level mirrored allele B fractions (mBAFs)

normalizePrincipalCurve.matrix

Fit a principal curve in K dimensions

TotalCnKernelSmoothing

The TotalCnKernelSmoothing class

PairedPscbsModel

The PairedPscbsModel class

TotalCnSmoothing

The abstract TotalCnSmoothing class

process.MultiSourceCopyNumberNormalization

Normalizes all samples

findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions

callXXorXY.numeric

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

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

getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file