callAllelicBalanceByDH.PairedPSCBS: Calls segments that are in allelic balance

In PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Calls segments that are in allelic balance

Description

Calls segments that are in allelic balance by thresholding on DH using a predetermined threshold. The variability of the DH mean levels is taken into account via a bootstrap estimator.

Usage

## S3 method for class 'PairedPSCBS'
callAllelicBalanceByDH(fit, delta=estimateDeltaAB(fit, flavor = "qq(DH)"), alpha=0.05,
  ..., verbose=FALSE)

Arguments

flavor	A character string specifying which type of call to use.
delta	(Tuning parameter) A non-negative numeric threshold.
alpha	A numeric in [0,1] specifying the upper and lower quantiles calculated by the bootstrap estimator.
...	Additional arguments passed to the bootstrap estimator *bootstrapTCNandDHByRegion().

Value

Returns a PairedPSCBS object with allelic-balance calls.

Algorithm

• Foo

• Bar

Author(s)

Henrik Bengtsson

See Also

Instead of calling this method explicitly, it is recommended to use the *callAllelicBalance() method.

PSCBS documentation built on May 29, 2024, 5:59 a.m.