shadowRegulon: Correction for pleiotropy

Description Usage Arguments Value

Description

This function penalyze the regulatory interactions based on pleiotropy analysis

Usage

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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


chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.