Calculating tumor-normal paired allele-specific copy number stratified on genotypes

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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

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 ## 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.

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