monster: MOdeling Network State Transitions from Expression and...

In dschlauch/MONSTER: Modeling Network State Transitions from Expression and Regulatory data (MONSTER)

Description

This function runs the MONSTER algorithm

Usage

monster(expr, design, motif = NULL, nullPerms = 100, numMaxCores = 1,
  outputDir = NA, ...)

Arguments

expr	Gene Expression dataset
design	Binary vector indicating case control partition
motif	Regulatory data.frame
nullPerms	number of random permutations to run (default 100). Set to 0 to only calculate observed transition matrix
numMaxCores	requires doParallel, foreach. Runs MONSTER in parallel computing environment. Set to 1 to avoid parallelization.
outputDir	save MONSTER results in a directory

Value

An object of class "monster" containing results

Examples

data(yeast)
design <- c(rep(0,ncol(yeast$exp.cc)), rep(1,ncol(yeast$exp.sr)))
monsterRes <- monster(cbind(yeast$exp.cc, yeast$exp.sr), 
    design, yeast$motif, nullPerms=10, numMaxCores=4)
plot(monsterRes)

dschlauch/MONSTER documentation built on May 15, 2019, 2:57 p.m.