Thanks. I just had a try following your suggestions. Based on the result, it seems that the "cc_seeds" are in the same order with "seedGenes"(which are described by gene symbols). Is this what you did in your code, or I just get such result by chance?
So the question is: when a seedGene list is upload by "vids", will the output be in the same order as seedGenes? If so, will other functions report the result in the same way as the function "transitivity"? cc_seeds=transitivity(myNetwork,type="local",isolates="NaN",vids=seedGenes) Many thanks Best Quanwei On 6/16/14 10:52 AM, "Gábor Csárdi" <csardi.ga...@gmail.com> wrote: >I believe I answered this already: > >http://lists.nongnu.org/archive/html/igraph-help/2014-06/msg00039.html > >Gabor > >On Mon, Jun 16, 2014 at 10:49 AM, Qunawei Zhang <qwzhang0...@gmail.com> >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=seedGene >>s) >> >> >> Thanks >> >> Best >> Quanwei >> >> >> _______________________________________________ >> igraph-help mailing list >> igraph-help@nongnu.org >> https://lists.nongnu.org/mailman/listinfo/igraph-help >> > >_______________________________________________ >igraph-help mailing list >igraph-help@nongnu.org >https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list igraph-help@nongnu.org https://lists.nongnu.org/mailman/listinfo/igraph-help
