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aroma.cn (version 1.3.3)

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

1.3.3

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

April 22nd, 2013

Functions in aroma.cn (1.3.3)

TotalCnSmoothing

The abstract TotalCnSmoothing class
MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class
normalizePrincipalCurve.matrix

Normalizes data in K dimensions using principal curves
PairedPscbsModel

The PairedPscbsModel class
Non-documented objects

Non-documented objects
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file
XYCurveNormalization

The XYCurveNormalization class
TumorBoostNormalization

The TumorBoostNormalization class
getSubsetToFit.MultiSourceCopyNumberNormalization

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

Calls regions that are copy neutral
normalizeBAFsByRegions.PairedPSCBS

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

The TotalCnBinnedSmoothing class
findAtomicAberrations.CopyNumberRegions

Finds all possible atomic regions
PrincipalCurveNormalization

The PrincipalCurveNormalization class
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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

Gets the names of all unique samples across all sources
callPeaks.PeaksAndValleys

Calls the peaks in peaks-and-valley estimates
aroma.cn-package

Package aroma.cn
testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region
calibrateC1C2.PairedPSCBS

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

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

Calls regions that are in allelic balance
callXXorXY.numeric

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

Simple creation of a CopyNumberRegions object
normalizeMirroredBAFsByRegions.matrix

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

Gets the list of data sets to be normalized
AbstractCurveNormalization

The AbstractCurveNormalization class
process.MultiSourceCopyNumberNormalization

Normalizes all samples