[igraph] Add 1st column of vertices to a subgraph where the 2nd column matches in the subgraph

[Benika H]

Hi everyone,

I need help adding a list of nodes to my subgraph that have the matching targets in my first graph.

here is my code so far.

hgnc_mapped.txt  looks like this 

ABCB7	FECH
ABCB7	GANAB

combined.txt looks like this

SNP/miRNA gene

hsa-let-7f-2 CCDC152

hsa-let-7f-2 CMAS

hsa-let-7f-2 MRPS35

edgeList <- read.table("~/Desktop/hgnc_mapped.txt", header=TRUE, sep="\t")

t <- as.data.frame(edgeList)

y <- graph.data.frame(t, directed=FALSE, vertices=NULL)

y <- simplify(y)

genelist <- read.table("~/Desktop/combined.txt", header=TRUE, sep="\t")

matches <- as.data.frame(genelist)

snps <- (matches$SNP.miRNA)

genes <- (matches$gene)

z <- graph.data.frame(matches, directed=FALSE, vertices=NULL)

wc <- walktrap.community(y, weights = edgeList$Weight, steps=20, merges =

                           TRUE, modularity = TRUE, membership = TRUE)

scc <- clusters(y, "strong")

vx_id = which(scc$csize<8 & scc$csize>=2)

vx_id

colors <- rainbow(max(membership(wc)))

V(y)$color <- membership(wc)

layout <- layout.kamada.kawai(y)

plot(y,layout=layout)

sub <- induced.subgraph(y,which(scc$membership %in% vx_id))

sub

sub <- add.vertices(sub, z[from=c(snps), to=c(genes), directed=TRUE, nv=1:length(z)])

When printing sub, it does not contain the new vertices.

Any help would be greatly appreciated.

Thanks in advance,

Beni