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
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