Description Usage Arguments Details Author(s) Examples
Find the degree distribution given edgelist (pair_id) and a list of proteins which degrees matter
1 | edgelist2degreeFreq(mitab, prots = NULL)
|
mitab |
data.table containing molecular interaction data, including pair_id |
prots |
list of relevant proteins, degree distribution is based on the prevalence of specific degrees in this list, all proteins in |
sep |
ID separator in pair_id, passed to |
unique pair_id is the unique identifier of the undirected interaction: ordered alphabetically and concatenated interacting molecule IDs cleanMITAB
Vitalii Kleshchevnikov
1 2 3 4 5 6 7 8 9 10 11 | if(F) {
# 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_freq = edgelist2degreeFreq(full)
plot(degree_freq$N, degree_freq$degree_freq,
log = "xy",
main = "degree distribution \n - human-human protein interactions -",
ylab = "degree frequency, log-scale",
xlab = "degree, log-scale",
las=1)
}
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