networkAnalysis: Identify enriched subnetworks
In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description Usage Arguments Details Value Author(s) References See Also Examples

This function finds subnetworks enriched for genes with significant phenotypes based on the package 'BioNet'.

1	networkAnalysis(pvalues, graph, fdr=0.001, verbose=TRUE)

`pvalues`	a numeric vector of p-values
`graph`	an object of class `graphNEL`, used as the interactome in the network analysis
`fdr`	a single numeric value specifying the false discovery for the scoring of nodes (see `BioNet::scoreNodes` and Dittrich et al., 2008 for details)
`verbose`	a single logical value indicating to display detailed messages (when verbose=TRUE) or not (when verbose=FALSE)

This function takes in a vector of p-values and a graph standing for the interactome to identify the maximum scoring subnetwork based on the BioNet package.

a subnetwork module of class graphNEL

Camille Terfve, Xin Wang

Beisser D, Klau GW, Dandekar T, Muller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30.

Dittrich MT, Klau GW, Rosenwald A., Dandekar T and Muller T. Identifying functional modules in protein-protein interaction networks: an integrated exact approach. Bioinformatics 2008 24(13):i223-i231.

networkPlot, viewSubNet, plotSubNet

## Not run: 
library(BioNet)
##load pvalues (see the vignette for details about the preprocessing of
##this data set)
data("KcViab_PVals")
##load interactome
data("Biogrid_DM_Interactome")
##identify subnetworks
enrichedSubNet <- networkAnalysis(pvalues=KcViab_PVals,
graph=Biogrid_DM_Interactome, fdr=0.001, verbose=TRUE)	

## End(Not run)