To run the simulation and analysis code:
reference/ESpresso
subdirectory.reference/submitter.sh
to construct a simulation function based on real data.simulations/submitter.sh
to perform the simulations for type I error control and power.
This assumes you have an LSF system, otherwise remove the bsub
preamble in front of each job to run it in a standard fashion.
The make_*_images.R
scripts are used to make plots of the simulation results.realdata/submitter.sh
to analyze the mESC data.
Individual R scripts in realdata
are also responsible for generating plots -- process_real.R
to generate barplots, plottop_ESpresso.R
for the top DE genes, and rank_ESpresso.R
to get the top DE pluripotency factors.The manuscript
directory contains all the LaTeX source code for the manuscript.
This can be compiled with make
.
The extrasim
directories contain other diagnostic scripts that were used to check the behaviour of certain methods.