callCopyNeutralByTCNofAB.PairedPSCBS: Calls regions that are copy neutral

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

Calls regions that are copy neutral

Description

Calls regions that are copy neutral from the total copy numbers (TCNs) of segments in allelic balance (AB).

Usage

## S3 method for class 'PairedPSCBS'
callCopyNeutralByTCNofAB(fit, delta=estimateDeltaCN(fit), alpha=0.05, ..., force=FALSE,
  verbose=FALSE)

Arguments

fit	A PairedPSCBS fit object as returned by segmentByPairedPSCBS.
delta	A non-negative double specifying the width of the "acceptance" region. Defaults to half of the distance between two integer TCN states, i.e. 1/2. This argument should be shrunken as a function of the amount of the normal contamination and other background signals.
alpha	A double in [0,0.5] specifying the significance level of the confidence intervals used.
...	Additional arguments passed to *calcStatsForCopyNeutralABs().
force	If TRUE, an already called object is skipped, otherwise not.
verbose	See Verbose.

Details

...

Value

Returns a PairedPSCBS fit object where a column with the copy-neutral call.

Author(s)

Henrik Bengtsson

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