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Question: Additional high-scoring subnetworks in BioNet
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gravatar for enricoferrero
15 months ago by
enricoferrero550
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()):

library(BioNet)
library(DLBCL)
data(dataLym)
data(interactome)

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)
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)
module
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
1
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
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