Calls regions that are copy neutral from the total copy numbers (TCNs) of segments in allelic balance (AB).
# S3 method for PairedPSCBS
callCopyNeutralByTCNofAB(fit, delta=estimateDeltaCN(fit), alpha=0.05, ..., force=FALSE,
verbose=FALSE)Returns a PairedPSCBS fit object where a column
with the copy-neutral call.
A PairedPSCBS fit object as returned by
segmentByPairedPSCBS.
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.
A double in [0,0.5] specifying the significance level
of the confidence intervals used.
Additional arguments passed to
*calcStatsForCopyNeutralABs().
If TRUE, an already called object is skipped, otherwise not.
See Verbose.
Henrik Bengtsson
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