viper (version 1.6.0)

msviperSynergy: msviper synergy analysis

Description

This function performs a synergy analysis for combinatorial regulation

Usage

msviperSynergy(mobj, per = 1000, seed = 1, cores = 1, verbose = TRUE)

Arguments

mobj

msviper object containing combinatorial regulation results generated by msviperCombinatorial

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

Value

Updated msviper object containing the sygergy p-value

See Also

msviper

Examples

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)