msviperCombinatorial {viper} | R Documentation |
This function performs combinatorial analysis for msviper objects
msviperCombinatorial(mobj, regulators = 100, nullmodel = NULL, minsize = NULL, adaptive.size = NULL, level = 10, cores = 1, processAll = FALSE, verbose = TRUE)
mobj |
msviper object generated by |
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 |
minsize |
Number indicating the minimum allowed size for the regulons, taken from |
adaptive.size |
Logical, whether the weight (likelihood) should be used for computing the size, taken from |
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 |
A msviper object
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)