nichenetr (version 0.1.0)

construct_tf_target_matrix: 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 {
 
# }
# 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)
# }