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Re: [igraph] "get.vertex.attribute(graph, name, index=V(graph))" ?

From: Gábor Csárdi
Subject: Re: [igraph] "get.vertex.attribute(graph, name, index=V(graph))" ?
Date: Mon, 16 Jun 2014 10:52:46 -0400

I believe I answered this already:



On Mon, Jun 16, 2014 at 10:49 AM, Qunawei Zhang <address@hidden> wrote:
> 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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