nichenet_ligand_target_matrix {OmnipathR} | R Documentation |
Creates a NicheNet ligand-target matrix
nichenet_ligand_target_matrix( weighted_networks, lr_network, optimized_parameters, use_weights = TRUE, construct_ligand_target_matrix_param = list() )
weighted_networks |
Weighted networks as provided by
|
lr_network |
A data frame with ligand-receptor interactions, as
produced by |
optimized_parameters |
The outcome of NicheNet parameter optimization
as produced by |
use_weights |
Logical: wether the network sources are weighted. In this function it only affects the output file name. |
construct_ligand_target_matrix_param |
Override parameters for
|
A matrix containing ligand-target probability scores.
networks <- nichenet_networks() expression <- nichenet_expression_data() optimization_results <- nichenet_optimization(networks, expression) nichenet_model <- nichenet_build_model(optimization_results, networks) lt_matrix <- nichenet_ligand_target_matrix( nichenet_model$weighted_networks, networks$lr_network, nichenet_model$optimized_parameters )