estimateDeltaAB.PairedPSCBS: Estimate a threshold for calling allelic balance from DH

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Estimate a threshold for calling allelic balance from DH

Description

Estimate a threshold for calling allelic balance from DH to be used by the *callAB() method.

Usage

## S3 method for class 'PairedPSCBS'
estimateDeltaAB(this, scale=NULL, flavor=c("qq(DH)", "q(DH)", "mad(hBAF)", "median(DH)"),
  ..., max=Inf, verbose=FALSE)

Arguments

scale	An optional numeric scale factor.
flavor	A character string specifying which type of estimator to use.
...	Additional arguments passed to the estimator.
max	(Optional) The maximum estimate allowed. If greater than this value, the estimate will be truncated.
verbose	See Verbose.

Value

Returns the threshold estimate as a numeric scalar.

Author(s)

Henrik Bengtsson

See Also

Internally, one of the following methods are used: *estimateDeltaABBySmallDH(), *estimateStdDevForHeterozygousBAF(), *estimateMeanForDH(), and *estimateHighDHQuantileAtAB().

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.