runPHONEMeS: Function to run PHONEMeS-ILP

In saezlab/PHONEMeS-ILP: Building logic-based models from discovery high-content phosphoproteomics data

Function to run PHONEMeS-ILP

Description

This function takes the PHONEMeS inputs (data object, background network, drug perturbation targets, experimental design and solver parameters) and returns the network solution

Arguments

targets.P	a list of drug targets
conditions	the experimental conditions from the data
inputObj	data inputs of PHONEMeS
experiments	which experimental conditions to consider for the analysis
bg	the background network
nK	a single string ("all","no", "drugs2data", "data") specifying whether the predicted edges should be included at all levels, none, only in the network that connects drug targets to data kinases or only between data sites and their kinases
solver	solver to use (either: cplex or cbc - cplex by default)
solverPath	path to solver (default: "/usr/bin/cplex")
nSolutions	number of solution to be returned by PHONEMeS (default: 100)
mipgap	CPLEX/Cbc parameter: the absolute tolerance on the gap between the best integer objective and the objective of the best node remaining. When this difference falls below the value of this parameter, the linear integer optimization is stopped. Default set to 0
relgap	CPLEX/Cbc parameter: Allowed relative gap of accepted solution comparing within the pool of accepted solution (fraction; default: 0)
replace	CPLEX parameter: Replacement strategy of solutions in the pool (0,1,2 - default: 2 = most diversified solutions)
populate	CPLEX parameter: Allowed number of solutions to be generated (default: 5000)
intensity	CPLEX parameter: Intensity of solution searching (0,1,2,3,4 - default: 4)
timelimit	CPLEX/Cbc parameter: Time limit of CPLEX optimisation (in seconds - default: 3600)
penFac	size penalty factor (default: 0.00001)

Value

This function returns the combined network solutions of PHONEMeS. It contains the Source, the Target and the Weight of each interaction. The Weight tells how frequently an interaction is present across the different solutioins.

Author(s)

E. Gjerga

saezlab/PHONEMeS-ILP documentation built on June 21, 2022, 5:36 p.m.