runPHONEMeS_Downsampling: Function to run PHONEMeS-ILP. Similar to runPHONEMeS, however...

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

Function to run PHONEMeS-ILP. Similar to runPHONEMeS, however the multiple solutions in this case are generated by running the PHONEMeS analysis multiple times with random downsampling of the data and then the solutions are combined in one consensus network.

Description

This function takes the PHONEMeS inputs 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")
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 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.