shadowRegulon {viper} | R Documentation |
This function penalyze the regulatory interactions based on pleiotropy analysis
shadowRegulon(ss, nes, regul, regulators = 0.05, shadow = 0.05, targets = 10, penalty = 2, method = c("absolute", "adaptive"))
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 |
Corrected regulon object