networkAnalysis {HTSanalyzeR} | R Documentation

## 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)

### 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.

### Value

a subnetwork module of class `graphNEL`

### Author(s)

Camille Terfve, Xin Wang

### 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)

[Package HTSanalyzeR version 2.38.0 Index]