compareNetworksWithFishersExactTest {ProCoNA} | R Documentation |
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
compareNetworksWithFishersExactTest(peps1, peps2, colors1, colors2, title = "", net1label = "", net2label = "")
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 |
Returns fishers exact test -log pvalues and overlap matrix showing the number of shared members for each pair of modules.
David L Gibbs
## 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)