compareNetworksWithFishersExactTest: compareNetworksWithFishersExactTest

In ProCoNA: Protein co-expression network analysis (ProCoNA).

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)

ProCoNA documentation built on Nov. 1, 2018, 3:28 a.m.