qp.analyse {qp}R Documentation

Performs some exploratory analyses on the q-partial graph

Description

Using the output of qp.search this function provides some exploratory analyses on the resulting q-partial graph.

Usage

qp.analyse(qp.output, threshold, largest.clique=TRUE, plot.image=TRUE)

Arguments

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

Details

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.

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.analyse(qp.out.bd5.N20.q10,threshold=0.9,largest.clique=TRUE)

[Package qp version 0.1-1 Index]