HTSanalyzeR (version 2.24.0)

networkAnalysis: Identify enriched subnetworks

Description

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

Usage

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

Arguments

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)

Value

a subnetwork module of class graphNEL

Details

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.

References

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.

See Also

networkPlot, viewSubNet, plotSubNet

Examples

## 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)