Question: Additional high-scoring subnetworks in BioNet
gravatar for enricoferrero
15 months ago by
United Kingdom
enricoferrero550 wrote:

I'd like to use BioNet to identify high-scoring subnetworks in my data.

The tutorial clearly explains how to identify the top scoring subnetwork (I don't have the CPLEX library so I'm using runFastHeinz()):


pvals <- cbind(t=dataLym$t.pval, s=dataLym$s.pval)
rownames(pvals) <- dataLym$label
pval <- aggrPvals(pvals, order=2, plot=FALSE)

subnet <- subNetwork(dataLym$label, interactome)
subnet <- rmSelfLoops(subnet)
A graphNEL graph with undirected edges
Number of Nodes = 2559
Number of Edges = 7788

fb <- fitBumModel(pval, plot=FALSE)
scores <- scoreNodes(subnet, fb, fdr=0.001)

module <- runFastHeinz(subnet, scores)
A graphNEL graph with undirected edges
Number of Nodes = 37
Number of Edges = 44

But what about other high-scoring subnetworks? It is likely that in a network with 2259 nodes there will be other interesting active subnetworks to explore other than the first one. How can I retrieve these?

Bonus question: are there any parameters that I can set to increase or decrease the size of the resulting subnetworks?

Thank you.

ADD COMMENTlink modified 15 months ago by branislav misovic120 • written 15 months ago by enricoferrero550
gravatar for branislav misovic
15 months ago by
Netherlands, Leiden
branislav misovic120 wrote:

hi  Enrico 
 Last year ,during the Networks course,  I  asked same question Gunnar W. Klau  (one of  the authors who worked with Heinz &  link to Cytoscape Examine plugin )   ,   he said :  "you can remove your 1st Module nodes from you PPI DB  and rerun the Heinz to get 2nd Module ... in the past Heinz  gave more than 1  Module" .
  I do not know the reason why they stopped providing that output .

ADD COMMENTlink written 15 months ago by branislav misovic120

Thanks Branislav, that sounds like a reasonable (although not ideal) workaround.

Hopefully someone from the dev team can step in and comment.

ADD REPLYlink written 15 months ago by enricoferrero550
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 176 users visited in the last hour