SIMoNe (Statistical Inference for MOdular NEtworks) is an R package which implements the inference of co-expression networks based on partial correlation coefficients from either steady-state or time-course transcriptomic data. Note that with both type of data this package can deal with samples collected in different experimental conditions and therefore not identically distributed. In this particular case, multiple but related graphs are inferred on one simone run.

The underlying statistical tools enter the framework of Gaussian graphical models (GGM). Basically, the algorithm searches for a latent clustering of the network to drive the selection of edges through an adaptive l1-penalization of the model likelihood.

The available inference methods for edges selection include

• neighborhood selection as in Meinshausen and Buhlman (2006), steady-state data only;
• graphical Lasso as in Banerjee et al, 2008 and Friedman et al (2008), steady-state data only;
• VAR(1) inference as in Charbonnier, Chiquet and Ambroise (2010), time-course data only;
• multitask learning as in Chiquet, Grandvalet and Ambroise (preprint), both time-course and steady-state data.

All the listed methods are based l1-norm penalization, with an additional grouping effect for multitask learning (including three variants: “intertwined”, “group-Lasso” and “cooperative-Lasso”).

The penalization of each individual edge may be weighted according to a latent clustering of the network, thus adapting the inference of the network to a particular topology. The clustering algorithm is performed by the mixer package, based upon Daudin, Picard and Robin (2008)'s Mixture Model for Random Graphs.

Since the choice of the network sparsity level remains a current issue in the framework of sparse Gaussian network inference, the algorithm provides a full path of estimators starting from an empty network and adding edges as the penalty level progressively decreases. Bayesian Information Criteria (BIC) and Akaike Information Criteria (AIC) are adapted to the GGM context in order to help to choose one particular network among this path of solutions.

Graphical tools are provided to summarize the results of a SIMoNe run and offer various representations for network plotting.

cancer_pooled.R

library(simone)
data(cancer)
str(cancer, max.level=1)
 
attach(cancer)
boxplot(expr, las=3, cex.axis=0.6)
table(status)
 
## no clustering by default
res.no <- simone(expr)
plot(res.no) ## "trop" de monde sur BIC / AIC
g.no <- getNetwork(res.no, 30)
plot(g.no)
plot(g.no, type = "cluster")
 
## try with clustering now
ctrl <- setOptions(clusters.crit=30)
res.cl <- simone(expr, clustering=TRUE, control=ctrl)
g.cl <- getNetwork(res.cl, 30)
plot(g.cl)
plot(g.cl, type = "circles")
 
## Let us compare the two networks
plot(g.no,g.cl)
plot(g.no,g.cl, type="overlap")

cancer_mtasks.R

library(simone)
data(cancer)
str(cancer, max.level=1)
 
attach(cancer)
boxplot(expr, las=3, cex.axis=0.6)
table(status)
 
out <- simone(expr, tasks=status)
 
plot(out)
 
glist <- getNetwork(out, "AIC")
plot(glist[[1]],glist[[2]])
glist <- getNetwork(out, "BIC")
plot(glist[[1]],glist[[2]])
glist <- getNetwork(out, 65)
plot(glist[[1]],glist[[2]])
plot(glist[[1]],glist[[2]], type="overlap")
 
detach(cancer)

Within R, just type

install.packages("simone")

Install the package via the CRAN or perform manual installation by downloading the source

R CMD INSTALL simone_1.0-2.tar.gz

Have a look at the documentation. You may also check the demos:

demo(cancer_pooled)
demo(cancer_multitask)
demo(check_glasso, echo=FALSE)
demo(simone_steadyState)
demo(simone_timeCourse)
demo(simone_multitask)

• bugs, maintenance, feedback, questions: julien.chiquet@genopole.cnrs.fr

J. Chiquet, Y. Grandvalet, and C. Ambroise (2010). Inferring multiple graphical structures, Statistics and Computing. http://dx.doi.org/10.1007/s11222-010-9191-2

C. Charbonnier, J. Chiquet, and C. Ambroise (2010). Weighted-Lasso for Structured Network Inference from Time Course Data. Statistical Applications in Genetics and Molecular Biology, vol. 9, iss. 1, article 15. http://www.bepress.com/sagmb/vol9/iss1/art15/

C. Ambroise, J. Chiquet, and C. Matias (2009). Inferring sparse Gaussian graphical models with latent structure. Electronic Journal of Statistics, vol. 3, pp. 205–238. http://dx.doi.org/10.1214/08-EJS314

O. Banerjee, L. El Ghaoui, A. d'Aspremont (2008). Model Selection Through Sparse Maximum Likelihood Estimation. Journal of Machine Learning Research, vol. 9, pp. 485–516. http://www.jmlr.org/papers/volume9/banerjee08a/banerjee08a.pdf

J. Friedman, T. Hastie and R. Tibshirani (2008). Sparse inverse covariance estimation with the graphical Lasso. Biostatistics, vol. 9(3), pp. 432–441. http://www-stat.stanford.edu/~tibs/ftp/graph.pdf

N. Meinshausen and P. Buhlmann (2006). High-dimensional graphs and variable selection with the Lasso. The Annals of Statistics, vol. 34(3), pp. 1436–1462. http://projecteuclid.org/DPubS/Repository/1.0/Disseminate?view=body&id=pdfview_1&handle=euclid.aos/1152540754

J.-J. Daudin, F.Picard and S. Robin, S. (2008). Mixture model for random graphs. Statistics and Computing, vol. 18(2), pp. 173–183. http://www.springerlink.com/content/9v6846342mu82x42/fulltext.pdf