PSCBS (version 0.38.4)

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 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.

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

• 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.

Details

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

See Also

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