UGgmm-class: Undirected Gaussian graphical Markov model

In rcastelo/qpgraph: Estimation of genetic and molecular regulatory networks from high-throughput genomics data

Undirected Gaussian graphical Markov model

Description

The "UGgmm" class is the class of undirected Gaussian graphical Markov models defined within the qpgraph package to store simulate and manipulate this type of graphical Markov models (GMMs).

An undirected Gaussian GMM is a family of multivariate normal distributions sharing a set of conditional independences encoded by means of an undirected graph. Further details can be found in the book of Lauritzen (1996).

Objects from the Class

Objects can be created by calls of the form UGgmm(g, ...) corresponding to constructor methods or rUGgmm(n, g, ...) corresponding to random simulation methods.

Slots

p:

Object of class "integer" storing the dimension of the undirected Gaussian GMM corresponding to the number of random variables.

g:

Object of class graphBAM-class storing the associated undirected labeled graph.

mean:

Object of class "numeric" storing the mean vector.

sigma:

Object of class dspMatrix-class storing the covariance matrix.

Methods

UGgmm(g)

Constructor method where g can be either an adjacency matrix or a graphBAM-class object.

rUGgmm(n, g)

Constructor simulation method that allows one to simulate undirected Gaussian GMMs where n is the number of GMMs to simulate and g can be either a graphParam object, an adjacency matrix or a graphBAM-class object.

names(x)

Accessor method to obtain the names of the elements in the object x that can be retrieved with the $ accessor operator.

$

Accessor operator to retrieve elements of the object in an analogous way to a list.

dim(x)

Dimension of the undirected Gaussian GMM corresponding to the total number of random variables.

dimnames(x)

Names of the random variables in the undirected Gaussian GMM.

show(object)

Method to display some bits of information about the input undirected Gaussian GMM specified in object.

summary(object)

Method to display a sumamry of the main features of the input undirected Gaussian GMM specified in object.

plot(x, ...)

Method to plot the undirected graph associated to the the input undirected Gaussian GMM specified in x. It uses the plotting capabilities from the Rgraphviz library to which further arguments specified in ... are further passed.

Author(s)

R. Castelo

References

Lauritzen, S.L. Graphical models. Oxford University Press, 1996.

See Also

HMgmm

rcastelo/qpgraph documentation built on Oct. 28, 2024, 5:15 a.m.