Hello: I have a question about "get.vertex.attribute(graph, name, index=V(graph))". My network is protein-protein interaction network (suppose I save my network as "myNetwork"). (1)By the following command, I can get all the genes in the network. Is the sequence in "allGenes" corresponding to node id in the network? That is, allGenes[1] --> node 1; allGenes[2] --> node 2,,allGenes[i] --> node i ? allGenes=get.vertex.attribute(myNetwork,name="name")
(2) I have some seed genes, which we are interested(noted as "seedGenes"). I calculated their clustering coefficient by the following command. But we can't see the gene symbol in the output (which is available when we calculate degrees). Is there some way we can map "cc_seeds" to "seedGenes"(I.e., gene symbols)? I know we can calculate the clustering coefficient for each gene, separately. But I am afraid it will cost more time. Any suggestions? cc_seeds=transitivity(myNetwork,type="local",isolates="NaN",vids=seedGenes) Thanks Best Quanwei
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