compareNetworksWithFishersExactTest {ProCoNA} | R Documentation

## compareNetworksWithFishersExactTest

### Description

Fisher's exact test is used pairwise on modules to compare two networks. The arguments to Fisher's exact test are given below.

n == number of entities in the network

m == number of entities in intersection of two modules

d1 == number of entities in module A but not in module B

d2 == number of entities in module B but not in module A

2x2 matrix for the test is then: m d1 d2 n-d1-d2-m

### Usage

    compareNetworksWithFishersExactTest(peps1, peps2, colors1, colors2,
        title = "", net1label = "", net2label = "")

### Arguments

`peps1` | Nodes in network 1, character vector
`peps2` | Nodes in network 2, character vector
`colors1` | modules for net 1
`colors2` | modules for net 2
`title` | Plot title
`net1label` | xlabel
`net2label` | ylabel

### Value

Returns fishers exact test -log pvalues and overlap matrix showing the number of shared members for each pair of modules.

### Author(s)

David L Gibbs

### Examples

    ## Not run:
    data(ProCoNA_Data)
    #net1 <- buildProconaNetwork("peptide network", peptideData, pow=12)
    #net2 <- buildProconaNetwork("peptide network", peptideData, pow=6)
    compareNetworksWithFishersExactTest(peptides(net1), peptides(net2),
    mergedColors(net1), mergedColors(net2), "network comparison", "net1", "net2")

    ## End(Not run)

[Package ProCoNA version 1.18.0 Index]