viper (version 1.6.0)

msviperCombinatorial: msviper combinatorial analysis

Description

This function performs combinatorial analysis for msviper objects

Usage

msviperCombinatorial(mobj, regulators = 100, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, level = 10, cores = 1, processAll = FALSE, verbose = TRUE)

Arguments

mobj

msviper object generated by msviper function

regulators

Either a number between 0 and 1 indicating the p-value cutoff for individual TFs to be included in the combinations analysis; (>1) indicating the number of top TFs to be included in the combinations analysis; or a vector of character strings indicating the TF IDs to be included in the analysis

nullmodel

Matrix of genes by permutations containing the NULL model signatures. Taken from mobj by default

minsize

Number indicating the minimum allowed size for the regulons, taken from mobj by default

adaptive.size

Logical, whether the weight (likelihood) should be used for computing the size, taken from mobj by default

level

Integer, maximum level of combinatorial regulation

cores

Integer indicating the number of cores to use (only 1 in Windows-based systems)

processAll

Logical, whether all pairs, even if not significant, should be processed for synergy

verbose

Logical, whether progression messages should be printed in the terminal

Value

A msviper object

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)
plot(mra, cex=.7)