pairedAlleleSpecificCopyNumbers: Calculating tumor-normal paired allele-specific copy number...

In HenrikBengtsson/aroma.light-BioC_release: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types

Description

Calculating tumor-normal paired allele-specific copy number stratified on genotypes. The method is a single-sample (single-pair) method. It requires paired tumor-normal parent-specific copy number signals.

Usage

 ## S3 method for class 'numeric'
pairedAlleleSpecificCopyNumbers(thetaT, betaT, thetaN, betaN,
  muN=callNaiveGenotypes(betaN), ...)

Arguments

thetaT, betaT	Theta and allele-B fraction signals for the tumor.
thetaN, betaN	Total and allele-B fraction signals for the matched normal.
muN	An optional vector of length J containing normal genotypes calls in (0,1/2,1,NA) for (AA,AB,BB).
...	Not used.

Value

Returns a data.frame with elements CT, betaT and muN.

Author(s)

Pierre Neuvial, Henrik Bengtsson

See Also

This definition of calculating tumor-normal paired ASCN is related to how the normalizeTumorBoost() method calculates normalized tumor BAFs.

HenrikBengtsson/aroma.light-BioC_release documentation built on May 7, 2019, 1:55 a.m.