runPHONEMeS_mult: Function to run the PHONEMeS-ILP method for time-resolved...

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

Function to run the PHONEMeS-ILP method for time-resolved phosphoproteomics data.

Description

This function takes the PHONEMeS inputs of the time-point variant (data object, background network, drug perturbation targets, experimental design dependent on the time-points and solver parameters) and returns the time-resolved 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")
nIter	number of iterations to run/solution to be returned by PHONEMeS (default: 100)
penFac	size penalty factor (default: 0.00001)

Value

This function returns the combined network solutions of the time-resolved variant of PHONEMeS. It contains the Source, the Target, the Weight and the Time-Point. The Weight tells how frequently an interaction is present across the different solutioins. The Time-Point tells after which time-point an interaction appears in the solution.

Author(s)

E. Gjerga

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