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From: | Gábor Csárdi |
Subject: | Re: [igraph] Extracting subnets automatically for further analysis based on metric scores |
Date: | Thu, 7 Mar 2013 23:14:32 -0500 |
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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