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 coexperssion network, I tried using different community detection methods and but I am unable to identify which community detection is good for obtaining clusters?.
After clustering how to rank the subclusters and save each subcluster in separate files.