Vanilla Class Reference

This class implements the Vanilla algorithm. More...

#include <reconciliation-algorithms.h>

Inheritance diagram for Vanilla:

List of all members.

Public Member Functions
	Vanilla (MyGraph &graph, MyPointSet &weights, double q, double maxIters, double epsilon, string output)
	Vanilla (vector< MyGraph > &graphs, double q, double maxIters, double epsilon, string outputPrefix)
virtual	~Vanilla ()
	Destructor.
virtual string	getName ()
	Return the name of the Vanilla algorithm.
Protected Member Functions
virtual void	_updateNodeWeightA (MyNode node)
	Update the weight of a node in the current graph according to the Vanilla update function.
virtual pair< double, double >	_computeEnergy ()
	Compute the node sum and edge sum from the Vanilla energy function.

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Detailed Description

This class implements the Vanilla algorithm.

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Constructor & Destructor Documentation

Vanilla::Vanilla	(	MyGraph &	graph,
		MyPointSet &	weights,
		double	q,
		double	maxIters,
		double	epsilon,
		string	output
	)		[inline]

Constructor for running the algorithm on a single network with multiple initial weights samples.

Parameters:

[in]	graph	The network on which to operate.
[in]	weights	The samples containing initial node weights.
[in]	q	The parameter q used by the algorithm.
[in]	maxIters	The maximum number of iterations to run the iterative reconciliation algorithms.
[in]	epsilon	A small value that defines part of the convergence criteria.
[in]	outputPrefix	A string to prepend to all output files.

Vanilla::Vanilla	(	vector< MyGraph > &	graphs,
		double	q,
		double	maxIters,
		double	epsilon,
		string	outputPrefix
	)		[inline]

Constructor for running the algorithm on multiple networks with no initial weights.

Parameters:

[in]	graphs	The networks on which to operate.
[in]	q	The parameter q used by the algorithm.
[in]	maxIters	The maximum number of iterations to run the iterative reconciliation algorithms.
[in]	epsilon	A small value that defines part of the convergence criteria.
[in]	outputPrefix	A string to prepend to all output files.

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Member Function Documentation

void Vanilla::_updateNodeWeightA

(

MyNode

v

)

[protected, virtual]

Update the weight of a node in the current graph according to the Vanilla update function.

In order to compute the state of any node in the network, GeneMANIA solves the following equation where f_{i} is the node score for gene i, y_{i} is the inital bias vale for gene i, and w_{ij} is the association weight between genes i and j. $f=min({i}{}(f_{i}-y_{i})^{2}+{i}{}{j}{}w_{ij}(f_{i}-f_{j})^{2}) This equation reduces down to $f(u)={y(u)+ w_{u}f(u)}{1+ w_{v}f(v)}$ For more information about this formula, see the paper (cited in the class documentation).

Implements AbstractSingleReconciliation.

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The documentation for this class was generated from the following files:

• /home/poirel/src/c++/biorithm/reconcile/reconciliation-algorithms.h
• /home/poirel/src/c++/biorithm/reconcile/reconciliation-algorithms.C