run_vanilla_phonemes: Run vanilla PHONEMeS (PHONEMeS v1.0.0)

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

Run vanilla PHONEMeS (PHONEMeS v1.0.0)

Description

The code for this function is comparable to the orginal PHONEMeS package. An unsigned kinase-substrate network is used as prior knowledge connecting perturbed kinases with phosphosites.

Usage

run_vanilla_phonemes(
  inputObj,
  measObj,
  netObj = phonemesKSN,
  rmNodes = NULL,
  pruning = FALSE,
  n_steps_pruning = 50,
  carnival_options
)

Arguments

inputObj	named vector of perturbation targets
measObj	named vector of the measurements
netObj	data frame of the prior knowledge network
rmNodes	character vector of nodes to remove from prior knowledge network
pruning	logic, set to TRUE if network should be pruned (default = FALSE)
n_steps_pruning	integer giving the order of the neighborhood
options	An object of type “list” defining the run parameters CARNIVAL in PHONEMeS. Use the default_phonemes_options function to create a list with default parameter settings. If cplex or cbc are chosen as the solver, the parameter solverPath needs to be supplied.

Value

List of CARNIVAL results and final inputObj, measObj, netObj used

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