PSCBS (version 0.63.0)

estimateDeltaAB.PairedPSCBS: 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 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 maxium estimate allowed. If greater than this value, the estimate will be truncated.

verbose

See Verbose.

Value

Returns the threshold estimate as a numeric scalar.

See Also

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