stringgaussnet (version 1.1)

pickSIMoNeParam:

Pick SIMoNe parameters

Description

A function to help in choosing the SIMoNe parameter, and most particularly which model criterion, with a series of plot.

Usage

pickSIMoNeParam(DEGeneExpr, ClusterMethod = F, NEdges = NA)

Arguments

DEGeneExpr

Object of class DEGeneExpr

ClusterMethod

Boolean variable indicating whether using clustering constraint or not

NEdges

If clustering constraint is used, on which number of edges to do it. If it is set to NA, the function chooses the number of edges by computing the mean between those with maximal AIC and BIC scores from network without clustering constraint.

Details

The series of plots are directly taken from the function plot() of simone package.

References

Chiquet, J. et al. SIMoNe Statistical Inference for MOdular NEtworks. Bioinforma. Oxf. Engl. 25, 417 (2009).

See Also

SIMoNeNet, SIMoNeNet.default, getSIMoNeNet, print.SIMoNeNet, summary.SIMoNeNet, export.SIMoNeNet, FilterEdges.SIMoNeNet

Examples

# data(SpADataExpression)
# data(SpADEGenes)
# SpAData<-DEGeneExpr(t(SpADataExpression),SpADEGenes)

# NodesForSIMoNe<-rownames(SpADEGenes)[1:17]
# GaussianSpAData<-DEGeneExpr(t(SpADataExpression[NodesForSIMoNe,]),SpADEGenes[NodesForSIMoNe,])

# pickSIMoNeParam(GaussianSpAData)

# GlobalSIMoNeNet<-getSIMoNeNet(GaussianSpAData)
# GlobalSIMoNeNet<-FilterEdges(GlobalSIMoNeNet,0.4)
# print(GlobalSIMoNeNet,5)
# summary(GlobalSIMoNeNet)
# plot(GlobalSIMoNeNet)

# export(GlobalSIMoNeNet,"GlobalSIMoNeNet",T)