Hello: I am using igraph to analyze protein-protein interaction network in R, and tying to calculate similarity between each gene pair by similarity.dice(). But the result is a matrix without gene symbol(I.e., the name of vertex), I don't know the value for one specific gene pair. So I firstly mapped the genes into ids (from 1 to n, where n is the gene number) and then describe the network by ids. Finally I used "read.graph(file="biggestComponent_id.txt",format="edge list") to input the network. But I found the ids seems different from the input ids (likely added by "1"). Would you give me an explanation? Thanks
Best Quanwei
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