qp.analyse {qp} | R Documentation |
Using the output of qp.search
this function provides some
exploratory analyses on the resulting q-partial graph.
qp.analyse(qp.output, threshold, largest.clique=TRUE, plot.image=TRUE)
qp.output |
output of qp.search |
threshold |
threshold on the minimum non-rejection rate required for edge removal |
largest.clique |
when this flag is set to TRUE it calculates the dimension of the largest clique |
plot.image |
when this flag is set it plots the incidence matrix resulting of thresholding the non-rejection rates |
Returns an object of the class matrix showing the number of selected edges, the number of edges of the complete graph and the percentage of selected edges. When largest.clique=TRUE it gives also the size of the largest clique and when plot.image=TRUE it plots the incidence matrix resulting of thresholding the non-rejection rates.
Beware that the combination or arguments largest.clique=TRUE and a threshold > 0.95 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.
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.analyse(qp.out.bd5.N20.q10,threshold=0.9,largest.clique=TRUE)