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

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

Estimate a threshold for calling LOH from DH

Description

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

Usage

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

Algorithm

• Grabs the segment-level C1 estimates.

• Calculate segment weights proportional to the number of heterozygous SNPs.

• Estimate the C1=1 location as the weighted median C1 for segments that have been called to be in allelic balance.

• Estimate the C1=0 location as the smallest C1 among segments that are not in allelic balance.

• Let the LOH threshold be the midpoint of the estimates C1=0 and C1=1 locations.

Author(s)

Henrik Bengtsson

See Also

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

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.