Question: How to rank subclusters of a gene co-expression network identifed through community detection algorithm in igraph R package
gravatar for aiswaryabioinfo
16 months ago by
aiswaryabioinfo20 wrote:

I have constructed a gene co-expression network from RNA-seq data. The network has more than 10000 nodes and more than 1 million edges.The network file as an edge list format of memory around 1gb which was created by calculating Pearson correlation of each gene pairs and gene pairs having correlation greater than 95% we're selected to create the edge list. The file is too large to run in Cytoscape due to limitation of computer configuration.

In R, I am able to calculate the topological properties of the network. And to cluster the gene co-experssion network, I tried using louvain community detection method as this algorithm showed high modularity compared to other community detection algorithm

After clustering how to rank the subclusters and save each subcluster in separate files.

ADD COMMENTlink written 16 months ago by aiswaryabioinfo20

You want to rank the communities / sub-clusters, but by which metric? When you create your Louvain object, you should be able to simply access different parameters in that (membership and modularity), and find a way to rank based on this information, if you wish.

ADD REPLYlink written 16 months ago by Kevin Blighe63k

I want to rank the sub-clusters using membership parameter and want to write an edge list file for each subcluster.

ADD REPLYlink written 16 months ago by aiswaryabioinfo20

"membership parameter" must simply be an assignment that indicates to which cluster/module/community each gene belongs. For outputting an edge list, you can search for the answer with your search engine of choice - the answer will be there waiting for you. Just search for igraph output edge list

ADD REPLYlink written 16 months ago by Kevin Blighe63k
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