findHeinzMWCS: use the heinz algorithm to find a solution to the maximum...

View source: R/heinzWrapper.R

findHeinzMWCSR Documentation

use the heinz algorithm to find a solution to the maximum weight connected subgraph problem

Description

heinz ("heavy induced subgraphs") computes solutions to the maximum-weight connected subgraph problem.

Usage

findHeinzMWCS(
  searchGraph_igraph,
  n.threads = 2,
  induceSubgraph = FALSE,
  verbose = TRUE,
  timeLimit = 600
)

Arguments

searchGraph_igraph

The igraph representation of the graph that we look to search over with the MWCS solver

n.threads

Specifies the maximum number of threads that the heinz binary can use

induceSubgraph

Flag to dictate if you would prefer a tree or the induced subgraph of the solution

verbose

A flag that specifies if you want information on what the function is doing

timeLimit

The maximum number of seconds that the heinz binary should be allowed to run for (default: 600 seconds)

Value

igraphModule An igraph representation of the solution (with induced edges from the original search graph if requested)

References

An algorithmic framework for the exact solution of the prize-collecting Steiner tree problem. Mathematical Programming, Series B, 105(2-3):427-449, 2006, by I. Ljubic, R. Weiskircher, U. Pferschy, G. Klau, P. Mutzel, and M. Fischetti.

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

D. Beisser, G. W. Klau, T. Dandekar, T. Mueller and M. Dittrich (2010) BioNet: an R-package for the Functional Analysis of Biological Networks. Bioinformatics 26:08. 1129-1130 Apr.


adamsardar/stoneTrees documentation built on May 20, 2022, 7:38 p.m.