Code and Usage

We are moving the source code to GP-DREAM. Go here for the latest versions . We also have a preliminary version that can be run on GP-DREAM!
Source code
NEW: We have made the Hierarchical clustering part of MERLIN faster and less memory expensive. Please download the newest version of MERLIN
merlin.tgz After downloading type

tar -xvzf merlin.tgz

This will create a directory in the current path called merlin. cd in to the directory and type make. The executable is named learnMERLIN.
Third party libraries
MERLIN needs GNU scientific library to run. We provide libraries compiled x84 64 bit Linux platform.
./learnMERLIN -m example/in/yeast_expr_interpolated -o example/out/ -r4 -p-5 -h 0.6 -l example/in/regulators.txt -v1 -c example/in/clusterassign.txt -k300
There are several arguments merlin takes, however, the most important ones are r, p, h, v, c and l described below. We are working on improving the documentation and usability of merlin :
  • -m model
  • -o outputdir
  • -k maxfactorsize
  • -v cross_validation_cnt
  • -l restricted_regulator_fname
  • -p sparsity_prior
  • -r modularity_prior
  • -c initial_cluster_assignments
MERLIN uses the .data and .model format originally introduced with the Bayesian network learning in PNL (Probabilistic Network Library). We are providing a utility program called merlinconverter than can be used to convert the expression data matrix into .data and .model format. The directory has a minimal README with usage to show how to use the program
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