Re: [igraph] Find communities of a list of seed nodes and next 8 interactions in the community

[Gábor Csárdi]

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 <address@hidden> 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

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