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
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