Copy-Number Analysis of Large Microarray Data Sets
The AbstractCurveNormalization class
Package aroma.cn
Calls regions that are in allelic balance
Calls regions that are copy neutral
Calls the peaks in peaks-and-valley estimates
Calls XX or XY from ChrX allele B fractions of a normal sample
Simple creation of a CopyNumberRegions object
Gets a list of data files for a particular name across several data se...
Finds all possible atomic regions
Fits the multi-source model for one sample
Gets the names of all unique samples across all sources
Gets the UGP file specifying the common set of loci to normalize at
Gets the list of data sets to be normalized
Gets the data sets smoothed toward the UGP file
Gets subset of (smoothing) units for fitting the model
The MultiSourceCopyNumberNormalization class
Non-documented objects
Normalizes allele B fractions (BAFs) based on region-based PSCN estima...
Normalizes region-level mirrored allele B fractions (mBAFs)
Normalizes data in K dimensions using principal curves
The PairedPscbsModel class
The PrincipalCurveNormalization class
Normalizes all samples
Tests for allelic balance in a genomic region
The TotalCnBinnedSmoothing class
The TotalCnKernelSmoothing class
The abstract TotalCnSmoothing class
The TumorBoostNormalization class
The XYCurveNormalization class
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.
Useful links