MinDistParam: Constructor for 'MinDistParam' class

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Description

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

Usage

MinDistParam(nMAD = 0.75, dnacopy = DNAcopyParam(),
  penncnv = PennParam(), emission = EmissionParam(), thin = 10L)

Arguments

nMAD	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.
dnacopy	an object of class DNAcopyParam.
penncnv	probabilities/parameters of the PennCNV hidden Markov model
emission	an object of class EmissionParam
thin	a length-one vector indicating whether to thin the data. This is primarily for internal use in conjunction with the filterExperiment function.

See Also

segment

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.