msviperSynergy {viper} | R Documentation |
This function performs a synergy analysis for combinatorial regulation
msviperSynergy(mobj, per = 1000, seed = 1, cores = 1, verbose = TRUE)
mobj |
msviper object containing combinatorial regulation results generated by |
per |
Integer indicating the number of permutations |
seed |
Integer indicating the seed for the permutations, 0 for disable it |
cores |
Integer indicating the number of cores to use (only 1 in Windows-based systems) |
verbose |
Logical, whether progression messages should be printed in the terminal |
Updated msviper object containing the sygergy p-value
data(bcellViper, package="bcellViper") sig <- rowTtest(dset, "description", c("CB", "CC"), "N")$statistic dnull <- ttestNull(dset, "description", c("CB", "CC"), "N", per=100) # Only 100 permutations to reduce computation time, but it is recommended to perform at least 1000 permutations mra <- msviper(sig, regulon, dnull) mra <- msviperCombinatorial(mra, 20) mra <- msviperSynergy(mra) summary(mra)