PSCBS (version 0.35.6)

bootstrapTCNandDHByRegion.PairedPSCBS: Estimate confidence intervals of TCN and DH segment levels

Description

Estimate confidence intervals of TCN and DH segment levels using bootstrap.

Usage

## S3 method for class 'PairedPSCBS':
bootstrapTCNandDHByRegion(fit, B=1000L, probs=c(0.025, 0.05, 0.95, 0.975), statsFcn=NULL,
  by=c("betaTN", "betaT"), force=FALSE, seed=NULL, verbose=FALSE, .debug=FALSE, ...)

Arguments

B

A postive integer specifying the number of bootstrap samples.

probs

The default quantiles to be estimated.

statsFcn

A (optional) function that estimates confidence intervals given locus-level data. If NULL, the qu

by

A character specifying whether DH should be calculated from normalized ('betaTN') or non-normalized ('betaT') tumor BAFs.

force

If TRUE, already existing estimates are ignored, otherwise not.

seed

(optional) A random seed.

verbose

See Verbose.

.debug

(internal) If TRUE, additional sanity checks are performed internally..

...

Not used.

Value

• Returns a PairedPSCBS object with copy-neutral calls.

See Also

Internally, one of the following methods are used: *callCopyNeutralByTCNofAB().