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PSCBS (version 0.38.4)

callCopyNeutralByTCNofAB.PairedPSCBS: 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 functi
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.

Value

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

Details

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