build_proxy_structure: Build augmented structure comprising CM and CP values from...

In ptrcksn/BINDER: BayesIan gene regulatory Networks inferreD via gene coExpression and compaRative genomics

Description

Build augmented structure comprising CM and CP values from coexpression, ME and PE values.

Usage

build_proxy_structure(proxy_regulon, coexpression, O = NULL,
  delta_CM = "auto", delta_CP = "auto")

Arguments

proxy_regulon	Data frame comprising columns: regulator, target_candidate, ortholog_module_status (1 if orthologous, 0 otherwise), ME (1 if high affinity for regulator motif, 0 otherwise) and PE (1 if orthologous interaction, 0 otherwise).
coexpression	Numerical symmetric matrix providing gene coexpression values.
O	Named list where each name is a target candidate and each element is a character vector comprising names of genes that should not be included in the computation of CM and CP for the corresponding target candidate name; by default only autocoexpression is excluded.
delta_CM	Numerical cutoff point for coexpression module for CM: any values above threshold are considered to form a coexpression module with target_candidate; defaults to "auto" which represents the 95th percentile of coexpression scores involving target_candidate.
delta_CP	Numerical cutoff point for coexpression module for CM: any values above threshold are considered to form a coexpression module with target_candidate; defaults to "auto" which represents the 95th percentile of coexpression scores involving target_candidate.

Value

Data frame implementing augmented structure comprising columns: regulator, target_candidate, ortholog_module_status (1 if orthologous, 0 otherwise), ME (1 if high affinity for regulator motif, 0 otherwise), PE (1 if orthologous interaction, 0 otherwise), CM and CP.

ptrcksn/BINDER documentation built on Nov. 5, 2019, 1:56 a.m.