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aroma.cn (version 1.6.1)

Copy-Number Analysis of Large Microarray Data Sets

Description

Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.

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Install

install.packages('aroma.cn')

Monthly Downloads

348

Version

1.6.1

License

LGPL (>= 2.1)

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Maintainer

Henrik Bengtsson

Last Published

October 28th, 2015

Functions in aroma.cn (1.6.1)

aroma.cn-package

Package aroma.cn
callPeaks.PeaksAndValleys

Calls the peaks in peaks-and-valley estimates
findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral
TumorBoostNormalization

The TumorBoostNormalization class
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
PrincipalCurveNormalization

The PrincipalCurveNormalization class
TotalCnBinnedSmoothing

The TotalCnBinnedSmoothing class
XYCurveNormalization

The XYCurveNormalization class
fitOne.MultiSourceCopyNumberNormalization

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

Normalizes all samples
callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources
getSubsetToFit.MultiSourceCopyNumberNormalization

Gets subset of (smoothing) units for fitting the model
normalizeBAFsByRegions.PairedPSCBS

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

Normalizes data in K dimensions using principal curves
TotalCnSmoothing

The abstract TotalCnSmoothing class
callXXorXY.numeric

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

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

Gets the list of data sets to be normalized
testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region
normalizeMirroredBAFsByRegions.matrix

Normalizes region-level mirrored allele B fractions (mBAFs)
Non-documented objects

Non-documented objects
PairedPscbsModel

The PairedPscbsModel class
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
cnr

Simple creation of a CopyNumberRegions object
AbstractCurveNormalization

The AbstractCurveNormalization class
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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

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