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aroma.cn (version 1.7.1)

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.packages('aroma.cn')

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Version

1.7.1

License

LGPL (>= 2.1)

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Maintainer

Henrik Bengtsson

Last Published

February 17th, 2024

Functions in aroma.cn (1.7.1)

callAllelicBalanceByBAFs.PairedPSCBS

Calls regions that are in allelic balance
callPeaks.PeaksAndValleys

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

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

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

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

Finds all possible atomic regions
testAllelicBalanceByBAFs

Tests for allelic balance in a genomic region
cnr

Simple creation of a CopyNumberRegions object
getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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

Gets the data sets smoothed toward the UGP file
normalizeMirroredBAFsByRegions.matrix

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

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

Gets subset of (smoothing) units for fitting the model
process.MultiSourceCopyNumberNormalization

Normalizes all samples
normalizePrincipalCurve.matrix

Normalizes data in K dimensions using principal curves
getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized
PrincipalCurveNormalization

The PrincipalCurveNormalization class
TotalCnKernelSmoothing

The TotalCnKernelSmoothing class
PairedPscbsModel

The PairedPscbsModel class
AbstractCurveNormalization

The AbstractCurveNormalization class
Non-documented objects

Non-documented objects
TotalCnBinnedSmoothing

The TotalCnBinnedSmoothing class
callXXorXY.numeric

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

The MultiSourceCopyNumberNormalization class
XYCurveNormalization

The XYCurveNormalization class
aroma.cn-package

Package aroma.cn
TotalCnSmoothing

The abstract TotalCnSmoothing class
callCopyNeutralRegions.PairedPSCBS

Calls regions that are copy neutral
TumorBoostNormalization

The TumorBoostNormalization class