runBioNet {SMITE} | R Documentation

## Perform BioNet Analysis on a PvalueAnnotation

### Description

With BioNet, a researcher can find a single interconnected gene module using the highest scoring genes generated in a PvalueAnnotation. This function will load the module into the PvalueAnnotation for visualization and downstream analysis.

### Usage

    runBioNet(pvalue_annotation, network, alpha = 0.05)

### Arguments

`pvalue_annotation` | An S4 object of class PvalueAnnotation that has already had scores generated.
`network` | An interaction network of class graphNEL or igraph.
`alpha` | A numeric specfiying a cutoff for high scoring genes to be return with the highScores function.

### Details

The input of p-values to BioNet discussed in the BioNet vignette involves first modeling p-values as a Beta-uniform mixture model to obtain the actual corresponding probability function values. Since our scoring method produces p-values/scores that are uniform in distribution, we input them directly into the BioNet algorithm. For more details on BioNet see the reference or runFastHeinz in the BioNet package.

### Value

A PvalueAnnotation with a loaded module.

### Note

This is a wrapper function to run BioNet. The actual BioNet code was created by Beisser et al.

### Author(s)

N. Ari Wijetunga

### References

Beisser et al. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30. doi: 10.1093/bioinformatics/btq089. Epub 2010 Feb 25.

### See Also

plotModule extractModule runGOseq

### Examples

    ## load test data ##
    data(test_annotation_score_data)

    ## NOTE: commented out for example.  See vignette for better explanation ##

    #load reactome network with gene symbols ##
    #load(system.file("data","Reactome.Symbol.Igraph.rda", package="SMITE"))

    ## run BioNet ##
    #test_annotation<-runBioNet(pvalue_annotation=test_annotation,
    #network = REACTOME)

    ## view module ##
    #extractModules(pvalue_annotation=test_annotation, 1)

    ## plot module ##
    #plotModule(pvalue_annotation=test_annotation, which.network=1)

[Package SMITE version 1.8.0 Index]