Relaxed Integer Linear Programming¶

Usage¶

Step 0. Download the GLPK library

https://www.gnu.org/software/glpk/

Step 1. Compile the C code

g++ -std=c++11 RIPL_simplex2_07_31.cc -o msdc -L/PATH/glpk/lib -I/PATH/glpk/include -lglpk

Step 2. Run the RILP method

./msdc foreground.list background.list motif_mapping.fimo

You can also use the python wrapper:

python MSDC_wrapper.py [input_matrix] [output_file_name] [pos_k] [neg_j]

Below is an example:

python MSDC_wrapper.py AP1.Motif_Selection_Paper.csv AP1_2_2 2 2

pos_k: the maximal uncovered percent of foreground set. Possible values are integers from 1 to 10, where 1 means 10%.

neg_j: the maximal covered percent of background set. Possible values are integers from 1 to 10, where 1 means 10%.