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
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