Nothing
# write tab delimited report with information about a TRM nodes.
writeTRMreport = function(graph, file, organism, target, query, sort.by = "symbol") {
x = V(graph)$name
map=.getMapFromOrg(organism)
res=select(map,keys=x,columns=c("SYMBOL","GENENAME"))
S=res$SYMBOL
S[is.na(S)] = ""
D=res$GENENAME
D[is.na(D)] = ""
grole = rep("bridge", length(x))
grole[x %in% query] = "enriched"
gtype = rep("query", length(x))
gtype[x %in% target] = "target"
family = sapply(getTFclassFromEntrezgene(x), function(z) if(length(z) > 0) paste(z, sep = " | ") else "")
d = data.frame("entrezgene" = x, symbol = S, role = grole, type = gtype, description = D, family = family, check.names = FALSE)
d = d[order(d[, sort.by], decreasing = TRUE),]
if(!missing(file))
write.table(d, file = file, sep = "\t", row.names = FALSE, quote = FALSE)
invisible(d)
}
# compare a list of graph all-against-all.
getSimilarityMatrix = function(g_list, type = "edges") {
type = match.arg(type, c("nodes", "edges"))
m = matrix(NA, nrow = length(g_list), ncol = length(g_list), dimnames = list(names(g_list), names(g_list)))
for(i in 1:length(g_list)) {
for(j in i:length(g_list)) {
#message(i, " vs ", j)
i_n = names(g_list)[i]
j_n = names(g_list)[j]
#message(i_n, " vs ", j_n)
i_g = g_list[[i_n]]
j_g = g_list[[j_n]]
if(!is.null(i_g) & !is.null(j_g)) {
gi = graph.intersection(i_g, j_g)
gu = graph.union(i_g, j_g)
switch(type,
nodes = {
t_n = vcount(gu)
c_n = vcount(gi)
p = 100*c_n/t_n
#if(length(p) == 0) p = 0
m[i_n, j_n] = p
m[j_n, i_n] = p
},
edges = {
t_e = ecount(gu)
c_e = ecount(gi)
p = 100*c_e/t_e
# if(length(p) == 0) p = 0
m[i_n, j_n] = p
m[j_n, i_n] = p
}
)
}
}
}
m
}
.dcor = function (x, use = "pairwise")
{
as.dist(1 - cor(t(x), use = use))
}
getSequencesFromGenome = function(BED, genome, append.id) {
requireNamespace("Biostrings")
s = Biostrings::getSeq(genome, names = BED$chr, start = BED$start, end = BED$end)
sn = paste(ifelse(!missing(append.id), append.id, ""), BED$chr, BED$start, BED$end, sep = "_")
names(s) = sn
s
}
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