MinDistParam {MinimumDistance} | R Documentation

## Constructor for `MinDistParam` class

### 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`

[Package MinimumDistance version 1.36.0 Index]