View source: R/application_prediction.R
predict_ligand_activities | R Documentation |
predict_ligand_activities
Predict activities of ligands in regulating expression of a gene set of interest. Ligand activities are defined as how well they predict the observed transcriptional response (i.e. gene set) according to the NicheNet model.
predict_ligand_activities(geneset, background_expressed_genes,ligand_target_matrix, potential_ligands, single = TRUE,...)
geneset |
Character vector of the gene symbols of genes of which the expression is potentially affected by ligands from the interacting cell. |
background_expressed_genes |
Character vector of gene symbols of the background, non-affected, genes (can contain the symbols of the affected genes as well). |
ligand_target_matrix |
The NicheNet ligand-target matrix denoting regulatory potential scores between ligands and targets (ligands in columns). |
potential_ligands |
Character vector giving the gene symbols of the potentially active ligands you want to define ligand activities for. |
single |
TRUE if you want to calculate ligand activity scores by considering every ligand individually (recommended). FALSE if you want to calculate ligand activity scores as variable importances of a multi-ligand classification model. |
... |
Additional parameters for get_multi_ligand_importances if single = FALSE. |
A tibble giving several ligand activity scores. Following columns in the tibble: $test_ligand, $auroc, $aupr and $pearson.
## 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")
geneset = c("SOCS2","SOCS3", "IRF1")
background_expressed_genes = c("SOCS2","SOCS3","IRF1","ICAM1","ID1","ID2","ID3")
ligand_activities = predict_ligand_activities(geneset = geneset, background_expressed_genes = background_expressed_genes, ligand_target_matrix = ligand_target_matrix, potential_ligands = potential_ligands)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.