qpgraph-package {qpgraph}R Documentation

The q-order partial correlation graph learning software, qpgraph.

Description

q-order partial correlation graphs, or qp-graphs for short, are undirected Gaussian graphical Markov models that represent q-order partial correlations. They are useful for learning undirected graphical Gaussian Markov models from data sets where the number of random variables p exceeds the available sample size n as, for instance, in the case of microarray data where they can be employed to reverse engineer a molecular regulatory network.

Details

Package: qp
Version: 0.99.6
Date: 05-02-2009
biocViews: Microarray, Statistics, GraphsAndNetworks
Suggests: mvtnorm, graph, Rgraphviz, annotate, genefilter, org.EcK12.eg.db
License: GPL version 2 or newer
URL: http://functionalgenomics.upf.edu/qp

Functions

This package provides an implementation of the procedures described in (Castelo and Roverato, 2006, 2008). An example of its use for reverse-engineering of transcriptional regulatory networks from microarray data is available in the vignette qpTxRegNet. This package is a contribution to the Bioconductor (Gentleman et al., 2004) and gR (Lauritzen, 2002) projects.

Author(s)

R. Castelo and A. Roverato

Maintainer: R. Castelo <robert.castelo@upf.edu>

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.

Castelo, R. and Roverato, A. Reverse engineering molecular regulatory networks from microarray data with qp-graphs. J. Comput. Biol., accepted, 2008.

Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., Hornik, K. Hothorn, T., Huber, W., Iacus, S., Irizarry, R., Leisch, F., Li, C., Maechler, M. Rosinni, A.J., Sawitzki, G., Smith, C., Smyth, G., Tierney, L., Yang, T.Y.H. and Zhang, J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5:R80, 2004.

Lauritzen, S.L. (2002). gRaphical Models in R. R News, 3(2)39.


[Package qpgraph version 1.0.0 Index]