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
    )

[Package OmnipathR version 3.0.0 Index]