nichenet_ligand_target_links {OmnipathR} | R Documentation

## Compiles a table with weighted ligand-target links

### Description

A wrapper around `nichenetr::get_weighted_ligand_target_links` to compile a data frame with weighted links from the top ligands to their top targets.

### Usage

    nichenet_ligand_target_links(
      ligand_activities,
      ligand_target_matrix,
      genes_of_interest,
      n_top_ligands = 42,
      n_top_targets = 250
    )

### Arguments

`ligand_activities` | Ligand activity table as produced by `nichenetr::predict_ligand_activities`.
`ligand_target_matrix` | Ligand-target matrix as produced by `nichenetr::construct_ligand_target_matrix` or the wrapper around it in the current package: `nichenet_ligand_target_matrix`.
`genes_of_interest` | Character vector with the gene symbols of the genes of interest. These are the genes in the receiver cell population that are potentially affected by ligands expressed by interacting cells (e.g. genes differentially expressed upon cell-cell interaction).
`n_top_ligands` | How many of the top ligands to include in the ligand-target table.
`n_top_targets` | For each ligand, how many of the top targets to include in the ligand-target table.

### Value

A tibble with columns ligand, target and weight (i.e. regulatory potential score).

### 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$optimized_parameters
    )
    ligand_activities <- nichenet_ligand_activities(
        ligand_target_matrix = lt_matrix,
        lr_network = networks$lr_network,
        # the rest of the parameters should come
        # from your transcriptomics data:
        expressed_genes_transmitter = expressed_genes_transmitter,
        expressed_genes_receiver = expressed_genes_receiver,
        genes_of_interest = genes_of_interest
    )
    lt_links <- nichenet_ligand_target_links(
        ligand_activities = ligand_activities,
        ligand_target_matrix = lt_matrix,
        genes_of_interest = genes_of_interest,
        n_top_ligands = 20,
        n_top_targets = 100
    )

[Package OmnipathR version 3.0.0 Index]