default_carnival_options: Setting Default CARNIVAL Options

In saezlab/PHONEMeS: tool to run PHONEMeS on phosphoproteomic data

Setting Default CARNIVAL Options

Description

Returns the default CARNIVAL options as a list. You can modify the elements of the list and then use it as an argument in run_phonemes. If you choose CPLEX or CBC, you must modify then the solverPath field and point to the CPLEX/CBC executable (See Details).

Usage

default_carnival_options(solver = NULL)

Arguments

solver

one of cplex (recommended, but require 3rd party tool), cbc (also require 3rd party tool) or lpSolve (only for small networks)

Details

PHONEMeS is dependent on CARNIVAL for exhibiting the signalling pathway optimisation which requires the interactive version of IBM Cplex, Gurobi or CBC-COIN solver as the network optimiser. The IBM ILOG Cplex is freely available through Academic Initiative here. Gurobi license is also free for academics, request a license following instructions here. The CBC solver is open source and freely available for any user, but has a significantly lower performance than CPLEX or Gurobi. Obtain CBC executable directly usable for cosmos here. Alternatively for small networks, users can rely on the freely available lpSolve R-package, which is automatically installed with the package.

Value

returns a list with all possible options implemented in CARNIVAL

Examples

# load and change default options:
my_options = default_carnival_options(solver = "cplex")

my_options$solverPath = "/Applications/CPLEX_Studio128/cplex/bin/x86-64_osx/cplex"
my_options$threads = 2
my_options$timelimit = 3600*15

saezlab/PHONEMeS documentation built on May 2, 2024, 11:12 a.m.