[igraph] Extracting subnets automatically for further analysis based on metric scores

[Alex Upton]

Hello all,

I have a query I hope that you could help me with. After creating my network, 
and calculating a number of metrics, I would then like to automatically extract 
the subnets of the nodes with the 10 lowest ranks for each ( I have ranked the 
nodes with the highest scores 1, so would like those nodes from 1 to 10).  This 
has been done as such:


wdrank1 <- rank(-wd1s)
brank1 <- rank(-wb1s)
crank1 <- rank(-c1s)
hrank1 <- rank(-h1s)
erank1 <- rank(-e1s)
lrank1 <- rank(-l1s)
drank1 <- rank(-d1s)


The names for these nodes are gene symbols, and the output of each of these 
objects is the list of all the genes with their ranks for that category. 

Previously I have used a crude approach to extract the subnets; seeing which 
gene symbols are the top ten, and then doing a bit of trial and error to find 
the node numerical ID that matches the gene symbol. What I would like is to 
take the top 10 gene symbols for each category, and then create the subnets for 
these 10 gene symbols automatically. Then, it would be helpful to output this 
to an edgelist with the nodes as gene symbols and not node numerical IDs, so 
that these lists can then be fed to a program for gene set enrichment analysis. 
Is there a way then that I can do this? Any help would be greatly appreciated.

Kind regards,

Alex

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Alex Upton, BEng, MRes, PG Cert Business Administration

PhD Researcher Biomedical Informatics, Signals and Systems 
School of Electronic, Electrical and Computer Engineering, 
College of Engineering and Physical Sciences, University of Birmingham
Edgbaston, Birmingham, B15 2TT, United Kingdom

Fax: +44 121 4144291 (school general office)
Email: address@hidden

Personal Web: http://postgrad.eee.bham.ac.uk/uptona/
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