qpgraph-package: Estimation of genetic and molecular regulatory networks from...

Description Functions Author(s) References


Estimate gene and eQTL networks from high-throughput expression and genotyping assays.


This package provides an implementation of the procedures described in (Castelo and Roverato, 2006, 2009) and (Tur, Roverato and Castelo, 2014). An example of its use for reverse-engineering of transcriptional regulatory networks from microarray data is available in the vignette qpTxRegNet and, the same directory, contains a pre-print of a book chapter describing the basic functionality of the package which serves the purpose of a basic users's guide. This package is a contribution to the Bioconductor (Gentleman et al., 2004) and gR (Lauritzen, 2002) projects.


R. Castelo and A. Roverato


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. 16(2):213-227, 2009.

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

Tur, I., Roverato, A. and Castelo, R. Mapping eQTL networks with mixed graphical Markov models. Genetics, 198:1377-1393, 2014.

qpgraph documentation built on Jan. 10, 2021, 2:01 a.m.