estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS: Estimate a threshold for calling LOH from DH

Description Usage Arguments Details Value Algorithm Author(s) See Also

Description

Estimate a threshold for calling LOH from DH based on the location of guessed C1=0 and C1=1 peaks.

Usage

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## S3 method for class 'PairedPSCBS'
estimateDeltaLOHByMinC1ForNonAB(this, midpoint=1/2, maxC=3 * (ploidy(this)/2), ...,
  verbose=FALSE)

Arguments

midpoint

A numeric scalar in [0,1] specifying the relative position of the midpoint between the estimated locations of C1=0 and C1=1 mean parameters.

maxC

Maximum total copy number of a segment in order to be included in the initial set of segments.

...

Not used.

verbose

See Verbose.

Details

This method requires that calls for allelic balances already have been me made, cf. *callAllelicBalance().

Value

Returns the estimated LOH treshold as a numeric scalar or -Inf. In case it is not possible to estimate the LOH threshold, then -Inf is returned.

Algorithm

Author(s)

Henrik Bengtsson

See Also

Instead of calling this method explicitly, it is recommended to use the *estimateDeltaLOH() method.


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