CONETT
Combinatorial optimization method for identification of conserved evolutionary trajectories in tumors
System Requirements
- make (version 3.81 or higher)
- g++ (GCC version 4.1.2 or higher)
- Gurobi Optimizer
Compiling CONETT
In the Makefile, set GUROBIROOT to the path of your root Gurobi folder.
Simply run make command in the root CONETT folder. It will create the executables.
Running CONETT
Usage:
./conett -p [input tumor graph] -g [gene sets to be used as seeds] -t [minimum seed recurrence] -e [subgraph tumor conservation rate] -i [permutation p-value iterations] -a [edge weight cutoff] -f [outputFolder]
| Parameters |
Description |
-p |
Tumor graph file which shows temporal order of alterations |
-g |
(optional) File of gene (sets) that should be used as seeds |
-t |
Minimum recurrence frequency of the seeds |
-e |
Minimum number of tumors that each node on the trajectory has to follow the seed in |
-i |
(optional) The number of iterations for experimental estimation of the p-value of the size of the largest subgraph |
-a |
Threshold for the edge confidence in the ILP formulation |
-f |
Output folder name; all output files are placed into this folder |
Example
./conett -p data/TRACERxDAGs_inac_singleRoot.txt -g SeedPathways.txt -t 10 -e 10 -f TRACERx_ccRCC_20191030 -a 0.85