msviperSynergy: msviper synergy analysis

In viper: Virtual Inference of Protein-activity by Enriched Regulon 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)

viper documentation built on Nov. 8, 2020, 7:37 p.m.