run_phonemes: Run PHONEMeS

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

Run PHONEMeS

Description

This function runs CARNIVAL with the input of phosphoproteomic data (phosphosites and kinases). The prior knowledge network used is the combination of protein-protein and protein-phosphosite interactions from omnipath. Before running CARNIVAL the network is pruned by removing nodes n_steps upstream and downstream of measurements and inputs, respectively.

Usage

run_phonemes(
  inputObj,
  measObj,
  netObj = phonemesPKN,
  rmNodes = NULL,
  pruning = TRUE,
  n_steps_pruning = 50,
  carnival_options
)

Arguments

inputObj	named vector of perturbation targets. Either 1 (up regulated) or -1 (down regulated)
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 (recommended)
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.