callAllelicBalanceByDH.PairedPSCBS: Calls segments that are in allelic balance

Description Usage Arguments Value Algorithm Author(s) See Also

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

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## 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

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 6, 2019, 1:05 a.m.