callCopyNeutralByTCNofAB.PairedPSCBS: Calls regions that are copy neutral

Description Usage Arguments Details Value Author(s)

Description

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

Usage

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## 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


PSCBS documentation built on May 6, 2019, 1:05 a.m.