nichenet_optimization {OmnipathR} | R Documentation |
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.
nichenet_optimization( networks, expression, make_multi_objective_function_param = list(), objective_function_param = list(), mlrmbo_optimization_param = list() )
networks |
A list with NicheNet format signaling, ligand-receptor
and gene regulatory networks as produced by
|
expression |
A list with expression data from ligand perturbation
experiments, as produced by |
make_multi_objective_function_param |
Override parameters for
|
objective_function_param |
Override additional arguments passed to the objective function. |
mlrmbo_optimization_param |
Override arguments for
|
A result object from the function ‘mlrMBO::mbo’. Among other things, this contains the optimal parameter settings, the output corresponding to every input etc.
networks <- nichenet_networks() expression <- nichenet_expression_data() optimization_results <- nichenet_optimization(networks, expression)