Local transitivity returns the results in the same order as the vertices in `vids`. If this is what you are asking.
Gabor On Mon, Jun 16, 2014 at 11:48 AM, Qunawei Zhang <[email protected]> wrote: > 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" <[email protected]> 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 <[email protected]> >>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,Š,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 >>> [email protected] >>> https://lists.nongnu.org/mailman/listinfo/igraph-help >>> >> >>_______________________________________________ >>igraph-help mailing list >>[email protected] >>https://lists.nongnu.org/mailman/listinfo/igraph-help > > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
