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aroma.cn (version 1.5.0)

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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Version

Install

install.packages('aroma.cn')

Monthly Downloads

269

Version

1.5.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

October 17th, 2013

Functions in aroma.cn (1.5.0)

aroma.cn-package

Package aroma.cn
deShearC1C2UNDERSCORE20120922.PairedPSCBS

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

The abstract TotalCnSmoothing class
callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
TotalCnBinnedSmoothing

The TotalCnBinnedSmoothing class
normalizePrincipalCurve.matrix

Normalizes data in K dimensions using principal curves
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
PrincipalCurveNormalization

The PrincipalCurveNormalization class
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
PairedPscbsModel

The PairedPscbsModel class
getSubsetToFit.MultiSourceCopyNumberNormalization

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

Tests for allelic balance in a genomic region
callPeaks.PeaksAndValleys

Calls the peaks in peaks-and-valley estimates
getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources
XYCurveNormalization

The XYCurveNormalization class
getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file
normalizeBAFsByRegions.PairedPSCBS

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

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

Calls regions that are copy neutral
process.MultiSourceCopyNumberNormalization

Normalizes all samples
normalizeMirroredBAFsByRegions.matrix

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

Gets a list of data files for a particular name across several data sets
Non-documented objects

Non-documented objects
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
callXXorXY.numeric

Calls XX or XY from ChrX allele B fractions of a normal sample
calibrateC1C2.PairedPSCBS

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

Simple creation of a CopyNumberRegions object
AbstractCurveNormalization

The AbstractCurveNormalization class