qpGraph-class: The qp-graph

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

The qp-graph

Description

The "qpGraph" class is the class to store and manipulate q-order (partial) correlation graphs, or qp-graphs for short. See Castelo and Roverato (2006, 2009) for a mathematical and statistical definition of a qp-graph.

In earlier versions 1.x of the qpgraph package there was a function called qpGraph() to obtain a qp-graph from a matrix of non-rejection rates. This function, as it was written, has been deprecated and replaced by this class and corresponding constructor methods of the same name. The main difference with respect to earlier 1.x versions is that the argument threshold is now called epsilon, the argument return.type has been removed and the current version returns an object of this class qpGraph described in this manual page.

Arguments

epsilon	maximum cutoff value met by the edges present in the qp-graph.
topPairs	number of edges from the top of the ranking, defined by the non-rejection rates in nrrMatrix, to use to form the resulting qp-graph. This parameter is incompatible with a value different from NULL in epsilon.
pairup.i	subset of vertices to pair up with subset pairup.j
pairup.j	subset of vertices to pair up with subset pairup.i
q	q-order employed to derive the input matrix of non-rejection rates nrrMatrix.
n	when the input matrix of non-rejection rates nrrMatrix has been estimated from data, this is the number of observations in the data set.

Objects from the Class

Objects can be created by calls of the form qpGraph(nrrMatrix, ...) corresponding to constructor methods that take as input a matrix of non-rejection rates, calculated with qpNrr.

Slots

p:

number of vertices, in one-to-one correspondence with random variables.

q:

order of the qp-graph, always smaller than p-2.

n:

when the qp-graph has been estimated from data, this is the number of observations in the data set, which must be larger than q+2.

epsilon:

maximum cutoff value of the non-rejection rate met by the edges that are present in the qp-graph.

g:

undirected graph structure of the qp-graph stored as a graphBAM-class object.

Methods

qpGraph(nrrMatrix, ...)

Constructor method where nrrMatrix is a matrix of non-rejection rates.

show(object)

Method to display some bits of information about the qp-graph stored in the input argument object.

Author(s)

R. Castelo

References

Castelo, R. and Roverato, A. A robust procedure for Gaussian graphical model search from microarray data with p larger than n, J. Mach. Learn. Res., 7:2621-2650, 2006.

Castelo, R. and Roverato, A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comp. Biol., 16(2):213-227, 2009.

See Also

qpNrr

rcastelo/qpgraph documentation built on Jan. 15, 2024, 12:21 a.m.