estimateDeltaLOHByMinC1ForNonAB.PairedPSCBS: 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 PairedPSCBS
estimateDeltaLOHByMinC1ForNonAB(this, midpoint=1/2, maxC=3 * (ploidy(this)/2), ...,
  verbose=FALSE)

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.

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.

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

Henrik Bengtsson

Details

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