Optimizes NicheNet model parameters — nichenet

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

if (FALSE) {
networks <- nichenet_networks()
expression <- nichenet_expression_data()
optimization_results <- nichenet_optimization(networks, expression)
}