runPHONEMeS_UD: Function to run the upside-down variant of PHONEMeS

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

Function to run the upside-down variant of PHONEMeS

Description

This function takes the PHONEMeS inputs of the upside-down variant (data object, background network, list of highly regulated kinases and experimental design) 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")
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.