infer_supporting_datasources: Get the data sources that support the specific interactions...

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

Get the data sources that support the specific interactions in the extracted ligand-target signaling subnetwork

Description

infer_supporting_datasources Get the data sources that support the specific interactions in the extracted ligand-target signaling subnetwork

Usage

infer_supporting_datasources(signaling_graph_list,lr_network, sig_network, gr_network)

Arguments

signaling_graph_list	A list of two elements: sig: a data frame/ tibble containg weighted ligand-receptor and signaling interactions (from, to, weight); and gr: a data frame/tibble containng weighted gene regulatory interactions (from, to, weight)
lr_network	A data frame / tibble containing ligand-receptor interactions (required columns: from, to, source)
sig_network	A data frame / tibble containing signaling interactions (required columns: from, to, source)
gr_network	A data frame / tibble containing gene regulatory interactions (required columns: from, to, source)

Value

A tibble with columns from, to, source and layer

Examples

## Not run: 
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2",c("IL4","IL13"))
ligand_tf_matrix = construct_ligand_tf_matrix(weighted_networks, ligands, ltf_cutoff = 0.99, algorithm = "PPR", damping_factor = 0.5,ligands_as_cols = TRUE)
all_ligands = c("BMP2")
all_targets = c("HEY1")
top_n_regulators = 2
ligand_target_signaling_list = get_ligand_signaling_path(ligand_tf_matrix,all_ligands,all_targets,top_n_regulators,weighted_networks)
data_source_info_network = infer_supporting_datasources(ligand_target_signaling_list, lr_network, sig_network, gr_network)

## End(Not run)

saeyslab/nichenetr documentation built on March 26, 2024, 9:22 a.m.