qpRndGraph: Undirected random d-regular graphs

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

Description

Samples an undirected d-regular graph approximately uniformly at random.

Usage

qpRndGraph(p=6, d=2, labels=1:p, exclude=NULL, verbose=FALSE,
           return.type=c("adjacency.matrix", "edge.list", "graphBAM", "graphNEL"),
           R.code.only=FALSE)

Arguments

p	number of vertices.
d	degree of every vertex.
labels	vertex labels.
exclude	vector of vertices inducing edges that should be excluded from the sampled d-regular graph.
verbose	show progress on the calculations.
return.type	class of object to be returned by the function
R.code.only	logical; if FALSE then the faster C implementation is used (default); if TRUE then only R code is executed.

Details

This function implements the algorithm from Steger and Wormald (1999) for sampling undirected d-regular graphs from a probability distribution of all d-regular graphs on p vertices which is approximately uniform. More concretely, for all vertex degree values d that grow as a small power of p, all d-regular graphs on p vertices will have in the limit the same probability as p grows large. Steger and Wormald (1999, pg. 396) believe that for d >> sqrt(p) the resulting probability distribution will no longer be approximately uniform.

This function is provided in order to generate a random undirected graph as input to the function qpG2Sigma which samples a random covariance matrix whose inverse (aka, precision matrix) has zeroes on those cells corresponding to the missing edges in the input graph. d-regular graphs are useful for working with synthetic graphical models for two reasons: one is that d-regular graph density is a linear function of d and the other is that the minimum connectivity degree of two disconnected vertices is an upper bound of their outer connectivity (see Castelo and Roverato, 2006, pg. 2646).

Value

The adjacency matrix of the resulting graph.

Author(s)

R. Castelo and A. Roverato

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.

Steger, A. and Wormald, N.C. Generating random regular graphs quickly, Combinatorics, Probab. and Comput., 8:377-396.

See Also

qpG2Sigma

Examples

set.seed(123)

A <- qpRndGraph(p=50, d=3)

summary(apply(A, 1, sum))

qpgraph documentation built on Jan. 10, 2021, 2:01 a.m.