nichenet_ligand_target_matrix {OmnipathR}

R Documentation

Creates a NicheNet ligand-target matrix

Description

Creates a NicheNet ligand-target matrix

Usage

nichenet_ligand_target_matrix(
  weighted_networks,
  lr_network,
  optimized_parameters,
  use_weights = TRUE,
  construct_ligand_target_matrix_param = list()
)

Arguments

weighted_networks	Weighted networks as provided by nichenet_build_model.
lr_network	A data frame with ligand-receptor interactions, as produced by nichenet_lr_network.
optimized_parameters	The outcome of NicheNet parameter optimization as produced by nichenet_build_model.
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 nichenetr::construct_ligand_target_matrix.

Value

A matrix containing ligand-target probability scores.

Examples

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
)

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