get_prioritization_tables: Use the information from the niche- and spatial differential...

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Use the information from the niche- and spatial differential expression analysis of ligand-senders and receptor-receivers pairs, in addition to the ligand activity prediction and ligand-target inferernce, in order to make a final ligand-receptor and ligand-target prioritization table.

Description

get_prioritization_tables Use the information from the niche- and spatial differential expression analysis of ligand-senders and receptor-receivers pairs, in addition to the ligand activity prediction and ligand-target inferernce, in order to make a final ligand-receptor and ligand-target prioritization table.

Usage

get_prioritization_tables(output_nichenet_analysis, prioritizing_weights)

Arguments

output_nichenet_analysis	List containing following data frames: DE_sender_receiver, ligand_scaled_receptor_expression_fraction_df, sender_spatial_DE_processed, receiver_spatial_DE_processed, ligand_activities_targets, DE_receiver_processed_targets, exprs_tbl_ligand, exprs_tbl_receptor, exprs_tbl_target
prioritizing_weights	Named numeric vector in the form of: #' prioritizing_weights = c("scaled_ligand_score" = 5,

Value

A list containing a prioritization table for ligand-receptor interactions, and one for ligand-target interactions

Examples

## Not run: 
prioritizing_weights = c("scaled_ligand_score" = 5,
output_nichenet_analysis = list(DE_sender_receiver = DE_sender_receiver, ligand_scaled_receptor_expression_fraction_df = ligand_scaled_receptor_expression_fraction_df, sender_spatial_DE_processed = sender_spatial_DE_processed, receiver_spatial_DE_processed = receiver_spatial_DE_processed,
prioritization_tables = get_prioritization_tables(output_nichenet_analysis, prioritizing_weights)

## End(Not run)

saeyslab/nichenetr documentation built on April 27, 2024, 9:24 p.m.