qp.clique {qp} | R Documentation |
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
qp.clique(qp.output, N, threshold.lim=c(0,1), breaks=5, plot.image=TRUE)
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:
|
plot.image |
when this flag is set to TRUE , the
qp.clique plot is produced |
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.
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 |
Robert Castelo and Alberto Roverato
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
data(jmlr06data) qp.clique(qp.out.bd5.N20.q10,20)