R>=3.6.0; package: doParallel
Modify your DNV table in 01.prepare.simulation.R, see data/06.denovo.annotated.txt as example.
Modify the pathway file name in 01.prepare.simulation.R, see data/genesets/ for ready to use files.
Then Run those scripts in command line step by step:
-1.Rscript 01.prepare.simulation.R
-2.Rscript 02.simulation.R $i where i is the random seed to produce one simulation, you need a for loop to produce as many times of simulations as you want
-3.Rscript 03.simulation.load.parallel.R Note this script require 48 cpu cores, modify the code if your machine does not have that many cpus, you also need to change the simulation_time to match your simulated times in step 2.
pathway.enrichment.results/ contains the csv formated files
data/genesets/significant.pathways.symbols.gmt contains the gmt file of significant pathways
to.cytoscape.edge.tsv and to.cytoscape.node.tsv can be used as input to cytoscape software for visualization and clustering analysis.