edgelist2degree: find the degree for each protein given cleaned molecular...

In vitkl/MItools: Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service

Description

find the degree for each protein given cleaned molecular interaction data

Usage

edgelist2degree_slow(mitab, sep = "\\|", order_by_degree = T)

Arguments

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: "\|"

Details

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

Value

sorted data.table containing degree for each of the nodes in the input, details: mitab

Author(s)

Vitalii Kleshchevnikov

Examples

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)
}

vitkl/MItools documentation built on May 29, 2019, 2:55 p.m.