Hello, I have a really big PPI network and I clustered the network. Is there a way to analyze each cluster to find metrics of each cluster such as closeness, degree etc. I want to treat each cluster as an independent network but I have 56 cluster so an automated library would be great. I searched but could not find such a library. Is there a way to do it?
I can use R, Python or Cytoscape for this task.
Thank you in advance.
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written
by
hkarakurt
2 answers
Take a look at the igraph package for R.
There's no function that will do everything you ask for in one go if that's what you mean. Otherwise, you can extract a subgraph corresponding to a list of nodes with the subgraph() function then indeed operate on the subgraphs in a loop (or in parallel).
Have a look at Cytoscape Analyzer http://manual.cytoscape.org/en/stable/Network_Analyzer.html. From the GUI of Cytoscape, it's very easy to run this functionality either on an entire or subset of the network. It computes different network properties including Node Degree Distribution, Betweenness Centrality, Closeness Centrality etc.
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