shadowRegulon: Correction for pleiotropy

In viper: Virtual Inference of Protein-activity by Enriched Regulon analysis

Description

This function penalyze the regulatory interactions based on pleiotropy analysis

Usage

shadowRegulon(ss, nes, regul, regulators = 0.05, shadow = 0.05,
  targets = 10, penalty = 2, method = c("absolute", "adaptive"))

Arguments

ss	Named vector containing the gene expression signature
nes	Named vector containing the normalized enrichment scores
regul	Regulon object
regulators	Number indicating the number of top regulators to consider for the analysis or the p-value threshold for considering significant regulators
shadow	Number indicating the p-value threshold for considering a significant shadow effect
targets	Integer indicating the minimal number of overlaping targets to consider a pair of regulators for pleiotropy analysis
penalty	Number higher than 1 indicating the penalty for the pleiotropic interactions. 1 = no penalty
method	Character string indicating the method to use for computing the pleiotropy, either absolute or adaptive

Value

Corrected regulon object

viper documentation built on Nov. 8, 2020, 7:37 p.m.