clusteringCNVs-class: Class '"clusteringCNVs"'

In CNVrd2: CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

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. [e-mail]

Examples

showClass("clusteringCNVs")

CNVrd2 documentation built on Nov. 8, 2020, 5:30 p.m.