nichenet_optimization {OmnipathR} | R Documentation

## Optimizes NicheNet model parameters

### Description

Optimize NicheNet method parameters, i.e. PageRank parameters and source weights, basedon a collection of experiments where the effect of a ligand on gene expression was measured.

### Usage

    nichenet_optimization(
      networks,
      expression,
      make_multi_objective_function_param = list(),
      objective_function_param = list(),
      mlrmbo_optimization_param = list()
    )

### Arguments

`networks` | A list with NicheNet format signaling, ligand-receptor and gene regulatory networks as produced by `nichenet_networks`.
`expression` | A list with expression data from ligand perturbation experiments, as produced by `nichenet_expression_data`.
`make_multi_objective_function_param` | Override parameters for `smoof::makeMultiObjectiveFunction`.
`objective_function_param` | Override additional arguments passed to the objective function.
`mlrmbo_optimization_param` | Override arguments for `nichenetr::mlrmbo_optimization`.

### Value

A result object from the function ‘mlrMBO::mbo’. Among other things, this contains the optimal parameter settings, the output corresponding to every input etc.

### Examples

    networks <- nichenet_networks()
    expression <- nichenet_expression_data()
    optimization_results <- nichenet_optimization(networks, expression)

[Package OmnipathR version 3.0.0 Index]