ProCoNA (version 1.10.0)

compareNetworksWithFishersExactTest: 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.

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)