MinDistParam

a length-one numeric vector indicating the minimal
number of median absolute deviations of the mean segmented minimum
distance from zero.  For non-zero segments (# median absolute
deviations > nMAD), maximum a posteriori estimates of the
parent-offspring copy number states are computed.  Segments with
minimum distance values near zero are not called as they are less
likely to correspond to regions with de novo copy number
alterations.

nMAD

an object of class <code>DNAcopyParam</code>.

dnacopy

probabilities/parameters of the PennCNV hidden
Markov model

penncnv

an object of class <code>EmissionParam</code>

emission

a length-one vector indicating whether to thin the
data. This is primarily for internal use in conjunction with the
<code>filterExperiment</code> function.

thin


The <code>MinDistParam</code> class contains parameters used for the
segmentation implemented in the <code>DNAcopy</code> package, parameters
extracted from the <code>PennCNV</code> HMM such as parent-offspring
transmission parobabilities (see citation below), and initial
values / parameters for computing emission probabilities.


Analysis of de novo copy number variants in trios from
high-dimensional genotyping platforms.

Robert Scharpf

MinimumDistance

A Package for De Novo CNV Detection in Case-Parent Trios

MinDistParam function

The <code>MinDistParam</code> class contains parameters used for the
segmentation implemented in the <code>DNAcopy</code> package, parameters
extracted from the <code>PennCNV</code> HMM such as parent-offspring
transmission parobabilities (see citation below), and initial
values / parameters for computing emission probabilities.

MinDistParam: Constructor for `MinDistParam` class

Description

Usage

Arguments

See Also