runHeinz: Start HEINZ

In assaron/BioNet: Routines for the functional analysis of biological networks

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.

Author(s)

Daniela Beisser

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

assaron/BioNet documentation built on Sept. 18, 2020, 12:02 a.m.