construct_tf_target_matrix: Construct a tf-target matrix.

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

Construct a tf-target matrix.

Description

construct_tf_target_matrix Convert integrated gene regulatory weighted network into matrix format.

Usage

construct_tf_target_matrix(weighted_networks, tfs_as_cols = FALSE, standalone_output = FALSE)

Arguments

weighted_networks	A list of two elements: lr_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)
tfs_as_cols	Indicate whether ligands should be in columns of the matrix and target genes in rows or vice versa. Default: FALSE
standalone_output	Indicate whether the ligand-tf matrix should be formatted in a way convenient to use alone (with gene symbols as row/colnames). Default: FALSE

Value

A matrix containing tf-target regulatory weights.

Examples

 ## Not run: 
## Generate the ligand-target matrix from loaded weighted_networks
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
tf_target = construct_tf_target_matrix(weighted_networks, tfs_as_cols = TRUE, standalone_output = TRUE)

## End(Not run)

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