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aroma.cn (version 0.5.0)

Copy-number analysis of large microarray data sets

Description

Package for analysis of copy-number estimates obtained from various platforms.

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Install

install.packages('aroma.cn')

Monthly Downloads

269

Version

0.5.0

License

LGPL (>= 2.1)

Maintainer

Henrik Bengtsson

Last Published

May 16th, 2010

Functions in aroma.cn (0.5.0)

MultiSourceCopyNumberNormalization

The MultiSourceCopyNumberNormalization class

getFitAromaUgpFile.MultiSourceCopyNumberNormalization

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

getInputDataSets.MultiSourceCopyNumberNormalization

Gets the list of data sets to be normalized

XYCurveNormalization

The XYCurveNormalization class

callXXorXY.numeric

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

TotalCnSmoothing

The abstract TotalCnSmoothing class

getSmoothedDataSets.MultiSourceCopyNumberNormalization

Gets the data sets smoothed toward the UGP file

TumorBoostNormalization

The TumorBoostNormalization class

AbstractCurveNormalization

The AbstractCurveNormalization class

process.MultiSourceCopyNumberNormalization

Normalizes all samples

Non-documented objects

PrincipalCurveNormalization

The PrincipalCurveNormalization class

aroma.cn-package

Package aroma.cn

getAllNames.MultiSourceCopyNumberNormalization

Gets the names of all unique samples across all sources

fitOne.MultiSourceCopyNumberNormalization

Fits the multi-source model for one sample

getSubsetToFit.MultiSourceCopyNumberNormalization

Gets subset of (smoothing) units for fitting the model

extractTupleOfDataFiles.MultiSourceCopyNumberNormalization

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

TotalCnKernelSmoothing

The TotalCnKernelSmoothing class