clusteringCNVs-class {CNVrd2} | R Documentation

## Class `"clusteringCNVs"`

### Description

This class is used to cluster segmentation scores into copy-number groups.

### Objects from the Class

Objects can be created by calls of the form `new("clusteringCNVs", ...)`.

### Slots

`x`:

  Object of class `"numeric"`.

`k`:

  Object of class `"numeric"` indicating a number of groups.

`p`:

  Object of class `"numericOrNULL"` indicating groups' proportions.

`m`:

  Object of class `"numericOrNULL"` indicating groups' means.

`sigma`:

  Object of class `"numericOrNULL"` indicating groups' standard deviations.

`small`:

  Object of class `"numeric"` indicating the value to stop the iteration process of the EM algorithm.

`nMax`:

  Object of class `"numeric"` indicating a maximum number of iterations.

`EV`:

  Object of class `"logical"` indicating whether all groups having equal variances or not (default).

`eee`:

  Object of class `"numeric"` indicating a pseudo value of 0.

`nmaxInit`:

  Object of class `"numeric"` indicating a number of iterations to obtain initial values.

`nChangeVariance`:

  Object of class `"numeric"` indicating a number of times to change from unequal variances to equal variances (“this option is used to avoid the EM algorithm being broken down if there is one (or a few) sample in a group”).

`verbose`:

  Object of class `"logical"` indicating whether printing out all loops.

`groupDistance`:

  Object of class `"numericOrNULL"` indicating the distance between groups.

### Methods

emnormalCNV

  `signature(Object = "clusteringCNVs")`: run the EM algorithm.

groupCNVs

  `signature(Object = "clusteringCNVs")`: cluster segmentation scores into groups.

searchGroupCNVs

  `signature(Object = "clusteringCNVs")`: identify a number of groups.

### Author(s)

Hoang Tan Nguyen, Tony R Merriman and MA Black. hoangtannguyenvn@gmail.com

### Examples

    showClass("clusteringCNVs")

[Package CNVrd2 version 1.20.0 Index]