Description Usage Arguments Details Value Author(s) Examples
find the degree for each protein given cleaned molecular interaction data
1 | edgelist2degree_slow(mitab, sep = "\\|", order_by_degree = T)
|
mitab |
data.table containing molecular interaction data, including "IDs_interactor_A" and "IDs_interactor_B" or "pair_id" |
sep |
how are individual interactors in the pair_id reparated? default: "\|" |
edgelist2degree
uses "IDs_interactor_A", "IDs_interactor_B" columns of a supplied data.table mitab
to compute the degree. mitab
can be generated using cleanMITAB
edgelist2degree_slow
uses pair_id to compute degree. Unique pair_id is the unique identifier of the undirected interaction: ordered alphabetically and concatenated interacting molecule IDs cleanMITAB
sorted data.table containing degree for each of the nodes in the input, details: mitab
Vitalii Kleshchevnikov
1 2 3 4 5 6 7 8 9 | edgelist = data.table(pair_id = paste0(rep(c("P", "Q", "R"), each = 30),
"|",
sample(rep(c("Z", "X", "F"), each = 30)), 1:90))
edgelist2degree_slow(edgelist)
{
# download full human interactome (clean = TRUE is necessary to produce the right input for edgelist2degree)
full = fullInteractome(taxid = "9606", database = "IntActFTP", format = "tab25", clean = TRUE, protein_only = TRUE)
degree = edgelist2degree(full$data)
}
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