I am not sure what you are trying to do here. Can you give a small example with the output you expect? Please also see http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
Gabor On Fri, Feb 6, 2015 at 9:55 AM, Benika H <[email protected]> wrote: > Hi everyone, > > I have a list of seed nodes in a file like such : hsa-let-7f-2 > hsa-let-7f-2 hsa-let-7f-2 hsa-let-7f-2 hsa-mir-106b hsa-mir-1180 > hsa-mir-1228 > hsa-mir-1248 hsa-mir-1248 > and I have my edgelist that looks like this: > MCCC1 MCCC2 MCCC2 AUH MCEE MUT MCEE PCCA MCF2 CAP1 hsa-mir-1228 > COG8 MCF2 COPA MCF2 COPB2 MCF2 DOCK2 MCF2 GNA13 MCF2 GNG2 > I want to find the communities that holds my seed nodes with at most 8 of > its closest interactions. > > I've tried the following lines: > genes <- read.table("~/Desktop/connected.txt", header=FALSE, sep="\t") > g=as.matrix(genes) > > y <- graph.edgelist(g, directed=FALSE) > > seeds <- read.table("~/Desktop/combined.txt", header=TRUE, sep="\t") > seeds <- as.data.frame(sedds) > seeds <- seeds$seednodes > > x <- which(farthest.nodes(g) %in% communities(sg) <= 9) > subg <- induced.subgraph > (graph=y,vids=unlist(neighborhood(graph=y,order=9,nodes=seednodes))) > > Both of these give me 3 communities and only one contains one of my seed > nodes, but when I look at the communities using communities(sg), I see more > than that. > > Any help would be greatly appreciated. > > > > Beni H > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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