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aroma.cn (version 0.7.3)

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

0.7.3

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

June 25th, 2011

Functions in aroma.cn (0.7.3)

AbstractCurveNormalization

The AbstractCurveNormalization class
callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
calibrateC1C2.PairedPSCBS

Calibrates ASCN signals in (C1,C2) space based on region-based PSCN estimates
deShearC1C2.PairedPSCBS

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

The XYCurveNormalization class
fitOne.MultiSourceCopyNumberNormalization

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

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

Tests for allelic balance in a genomic region
getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized
Non-documented objects

Non-documented objects
normalizeBAFsByRegions.PairedPSCBS

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

The abstract TotalCnSmoothing class
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
cnr

Simple creation of a CopyNumberRegions object
normalizeMirroredBAFsByRegions.matrix

Normalizes region-level mirrored allele B fractions (mBAFs)
callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral
getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
findNeutralCopyNumberState

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

Gets a list of data files for a particular name across several data sets
TumorBoostNormalization

The TumorBoostNormalization class
aroma.cn-package

Package aroma.cn
findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file
process.MultiSourceCopyNumberNormalization

Normalizes all samples
callXXorXY.numeric

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

The PrincipalCurveNormalization class
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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