qp.clique {qp}R Documentation

Relationship between non-rejection rate and maximum clique size

Description

Using the output of qp.search this function calculates the maximum clique size as a function of the minimum threshold on the non-rejection rate for removing an edge

Usage

qp.clique(qp.output, N, threshold.lim=c(0,1), breaks=5, plot.image=TRUE)

Arguments

qp.output output of qp.search
N sample size
threshold.lim range of the non-rejection rate threshold on which calculate the funcion
breaks one of:
  • a vector giving the breakpoints along the range defined by threshold.lim,
  • a single number giving the number of equidistant breakpoints that divide the range defined by threshold.lim.
plot.image when this flag is set to TRUE, the qp.clique plot is produced

Details

The qp.clique plot provides information on the graphs potentially selected by specifying different values of the threshold. Every circle in the plot corresponds to a graph and has three values associated with it: the threshold value used to construct the graph (horizontal axis); the number of vertices of the largest clique of the graph (vertical axis); the percentage of present edges in the graph (number inside the plot, beside the circle). Furthermore, adjacent circles are joined by a line and the dotted horizontal line corresponds to the sample size N.

Beware that setting breakpoints between 0.95 and 1.0 may result in a very long time of computation due to the NP-hardness of the problem of calculating the size of the largest clique.

Value

threshold threshold on the non-rejection rate that provides the maximum clique size that is strictly smaller than the sample size N
size maximum clique size strictly smaller than the sample size N

Author(s)

Robert Castelo and Alberto Roverato

References

Castelo, R. and Roverato, A. (2006). A robust procedure for Gaussian graphical model search from microarray data with p larger than n, J. Mach. Learn. Res., accepted

See Also

qp.search

Examples

data(jmlr06data)
qp.clique(qp.out.bd5.N20.q10,20)

[Package qp version 0.1-1 Index]