BioNet (version 1.32.0)

runHeinz: Start HEINZ

Description

The function starts HEINZ from command line. The HEINZ folder has to include the heinz.py python script and the dhea file. CPLEX has to be installed and accessible from the computer R runs on.

Usage

runHeinz(heinz.folder="", heinz.e.file, heinz.n.file, N=TRUE, E=FALSE, diff=-1, n=1)

Arguments

heinz.folder

The folder which contains the heinz.py python script and the dhea file.

heinz.e.file

The HEINZ edge input file. See writeHeinzEdges

heinz.n.file

The HEINZ node input file. See writeHeinzNodes

N

Boolean value, whether to run HEINZ on nodes.

E

Boolean value, whether to run HEINZ on edges. HEINZ can run on both with N and E set to TRUE.

diff

Difference of suboptimal solutions to optimal solution in haming distance in percent. Parameter is set to -1 for optimal solution.

n

Number of optimal and suboptimal solutions, the standard n=1 delivers only the optimal solution.

Details

This function starts the integer linear programming algorithm to calculate the optimal scoring subnetwork. The algorithm might be started in the command line when the CPLEX is installed on another machine. To start it from command line use: heinz.py -e edge.file.txt -n node.file.txt -E False/True -N False/True. The results can be loaded with readHeinzTree, readHeinzGraph as a graph object.

References

M. T. Dittrich, G. W. Klau, A. Rosenwald, T. Dandekar, T. Mueller (2008) Identifying functional modules in protein-protein interaction networks: an integrated exact approach. (ISMB2008) Bioinformatics, 24: 13. i223-i231 Jul.

See Also

writeHeinzEdges, writeHeinzNodes, readHeinzTree, readHeinzGraph