estimateKappaByC1Density.PairedPSCBS: Estimate global background in segmented copy numbers

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

Estimate global background in segmented copy numbers

Description

Estimate global background in segmented copy numbers based on the location of peaks in a weighted density estimator of the minor copy number mean levels.

The global background, here called \kappa, may have multiple origins where normal contamination is one, but not necessarily the only one.

Assumptions: This estimator assumes that there are segments with C1=0 and C1=1, i.e. some deletions and, typically, some normal segements.

Usage

## S3 method for class 'PairedPSCBS'
estimateKappaByC1Density(this, typeOfWeights=c("dhNbrOfLoci", "sqrt(dhNbrOfLoci)"),
  adjust=1, from=0, minDensity=0.2, ..., verbose=FALSE)

Arguments

typeOfWeights	A character string specifying how weights are calculated.
adjust	A numeric scale factor specifying the size of the bandwidth parameter used by the density estimator.
from	A numeric scalar specifying the lower bound for the support of the estimated density.
minDensity	A non-negative numeric threshold specifying the minimum density a peak should have in order to consider it a peak.
...	Not used.
verbose	See Verbose.

Value

Returns the background estimate as a numeric scalar.

Algorithm

• Retrieve segment-level minor copy numbers and corresponding weights:

  1. Grabs the segment-level C1 estimates.

  2. Calculate segment weights. The default (typeOfWeights="dhNbrOfLoci") is to use weights proportional to the number of heterozygous SNPs. An alternative (typeOfWeights="sqrt(dhNbrOfLoci)") is to use the square root of those counts.

• Identify subset of regions with C1=0:

  1. Estimates the weighted empirical density function (truncated at zero below). Tuning parameter 'adjust'.

  2. Find the first two peaks (with a density greater than tuning parameter 'minDensity').

  3. Assumes that the two peaks corresponds to C1=0 and C1=1.

  4. Defines threshold Delta0.5 as the center location between these two peaks.

• Estimate the global background signal:

  1. For all segments with C1 < Delta0.5, calculate the weighted median of their C1:s.

  2. Let kappa be the above weighted median. This is the estimated background.

Author(s)

Henrik Bengtsson

See Also

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

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