msviperCombinatorial: msviper combinatorial analysis

In chrischen1/viper_copy: Virtual Inference of Protein-activity by Enriched Regulon 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)

chrischen1/viper_copy documentation built on May 13, 2019, 6:52 p.m.