Version: 1.0 Date: June-17-2019 contact: bokhariya@vcu.edu tarodz@vcu.edu
Requirements:
- Matlab 2- GUROBI OPTIMIZATION Version:7 Note: Matlab should be directed to Gurobi directory
USAGE:
*utlRoulette, selectSubsetVer and Gurobi_optimization_nets are function needed and used in QuadMutNetEx
A- QuadMutNetEx:
INPUT :
Describtion of QuadMutNetEx arguments:
1- G:
Mutation matrix in a matlab sparse format. Patients have a serial number from 1 to m. Genes have serial number from 1 to n.
2- GenesNames:
vector of genes names orderd as in the G sparse matrix(from 1 to n).
3- nets:
a matrix of one or multiple binary networks added together.
4- t:
Integer number of iterations desired.
5- n:
Integer number of genes to be included in the submatrix G' each iteration. Each iteration a matrix G' is chosen rendomly
from the big matrix G.
6- c:
Parameter c (As c gets bigger as the number of genes in solution shrinks).
7- k:
Parameter k (High value of k panalize for overlap).
8- np:
Parameter np (High value of np increases the effect of the network(s)
9- GenesSelProb: (optional)
vector of probabilities of each gene to be chosen randomly.The probabilities should be in one column orderd as
created serial number in the G_file(from 1 to n). The sum of the
colmn should be equal 1.
Note: If left empty then each gene will have equal chance to be chosen
OUTPUT:
objective_function: Solution score that is the objective function we want to minimize.
x: Selected genes numbers as given and orderd in the sparse matrix
solutionSet: names of selected genes
subNetSol: SolutionSet submatrix of summations of matrix(es) nets.
see also QuadMutNetEx_Example.m