estimateKappaByC1Density.PairedPSCBS: Estimate global background in segmented copy numbers

Description Usage Arguments Value Algorithm Author(s) See Also

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 κ, 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

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## 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

Author(s)

Henrik Bengtsson

See Also

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


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