normalize_single_cell_ligand_activities: Normalize single-cell ligand activities

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

Normalize single-cell ligand activities

Description

normalize_single_cell_ligand_activities Normalize single-cell ligand activities to make ligand activities over different cells comparable.

Usage

normalize_single_cell_ligand_activities(ligand_activities)

Arguments

ligand_activities

Output from the function 'predict_single_cell_ligand_activities'.

Value

A tibble giving the normalized ligand activity scores for single cells. Following columns in the tibble: $cell, $ligand, $pearson, which is the normalized ligand activity value.

Examples

## Not run: 
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2","IL4")
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands, ltf_cutoff = 0, algorithm = "PPR", damping_factor = 0.5, secondary_targets = FALSE)
potential_ligands = c("TNF","BMP2","IL4")
genes = c("SOCS2","SOCS3","IRF1","ICAM1","ID1","ID2","ID3")
cell_ids = c("cell1","cell2")
expression_scaled = matrix(rnorm(length(genes)*2, sd = 0.5, mean = 0.5), nrow = 2)
rownames(expression_scaled) = cell_ids
colnames(expression_scaled) = genes
ligand_activities = predict_single_cell_ligand_activities(cell_ids = cell_ids, expression_scaled = expression_scaled, ligand_target_matrix = ligand_target_matrix, potential_ligands = potential_ligands)
normalized_ligand_activities = normalize_single_cell_ligand_activities(ligand_activities)

## End(Not run)

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