Parameters for ligand to target influence computation

Usage

params_ligand_target(
  lr_sig_hub = 0,
  gr_hub = 0,
  ltf_cutoff = 0.99,
  damping_factor = 0.5,
  tol = 1e-06,
  max_iter = 1000L,
  topology_correction = FALSE,
  secondary_targets = FALSE
)

Arguments

lr_sig_hub: Numeric. Numeric in [0, 1]. Hub correction strength for the ligand-receptor / signalling layer. 0 disables correction. Defaults to 0.0.
gr_hub: Numeric. Numeric in [0, 1]. Hub correction strength for the gene regulatory layer. 0 disables correction. Defaults to 0.0.
ltf_cutoff: Numeric. Numeric in [0, 1]. Quantile cutoff applied to the intermediate ligand-to-TF matrix. Defaults to 0.99.
damping_factor: Numeric. Numeric in [0, 1]. PageRank-style damping factor. Defaults to 0.5.
tol: Numeric. Numeric > 0. Convergence tolerance for the propagation step. Defaults to 1e-06.
max_iter: Integer. Integer >= 1. Maximum iterations for the propagation step. Defaults to 1000L.
topology_correction: Boolean. Apply topology correction. Defaults to FALSE.
secondary_targets: Boolean. Run a second round through targets. Defaults to FALSE.

Value

A named list with the following elements:

lr_sig_hub - Numeric. Numeric in [0, 1]. Hub correction strength for the ligand-receptor / signalling layer. 0 disables correction. Defaults to 0.0.
gr_hub - Numeric. Numeric in [0, 1]. Hub correction strength for the gene regulatory layer. 0 disables correction. Defaults to 0.0.
ltf_cutoff - Numeric. Numeric in [0, 1]. Quantile cutoff applied to the intermediate ligand-to-TF matrix. Defaults to 0.99.
damping_factor - Numeric. Numeric in [0, 1]. PageRank-style damping factor. Defaults to 0.5.
tol - Numeric. Numeric > 0. Convergence tolerance for the propagation step. Defaults to 1e-06.
max_iter - Integer. Integer >= 1. Maximum iterations for the propagation step. Defaults to 1000L.
topology_correction - Boolean. Apply topology correction. Defaults to FALSE.
secondary_targets - Boolean. Run a second round through targets. Defaults to FALSE.