This class implements the GenGO functional enrichment algorithm from the following paper: http://www.ncbi.nlm.nih.gov/pubmed/18676451. More...

Inheritance diagram for GenGOAlgorithm:

Classes
struct	FunctionInfo
Public Member Functions
	GenGOAlgorithm (const MyGraph &clusterGraph, const MyGraph &universeGraph, MyAnnotations &annotations, const GeneOntology &go, string category, double p, double q, double penalty)
	Default constructor.
virtual	~GenGOAlgorithm ()
	Default destructor.
virtual void	computeEnrichedFunctions (const set< string > &functionsToProcess)
	This method runs the GenGO algorithm.
virtual void	computeEnrichmentForFunction (const string funcType, const string funcId)
	Computes whether one function is enriched.
virtual void	printEnrichmentResults (ostream &ostr)
	prints the enrichment results

Detailed Description

This class implements the GenGO functional enrichment algorithm from the following paper: http://www.ncbi.nlm.nih.gov/pubmed/18676451.

Constructor & Destructor Documentation

GenGOAlgorithm::GenGOAlgorithm	(	const MyGraph &	clusterGraph,
		const MyGraph &	universeGraph,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category,
		double	p,
		double	q,
		double	penalty
	)

Default constructor.

Parameters:

[in]	clusterGraph	an instance of MyGraph storing the "cluster" for which we want to compute functional enrichment.
[in]	universeGraph	an instance of MyGraph storing the universe of genes.
[in]	annotations	The annotations for the genes.
[in]	p	The probability p for the GenGO algorithm.
[in]	q	The probability q for the GenGO algorithm.
[in]	penalty	The penalty for including a term in the final function set.

Warning:: clusterGraph should be a subgraph of universeGraph, but the class does not check this condition.

void GenGOAlgorithm::computeEnrichedFunctions ( const set< string > & functionsToProcess ) [virtual]

This method runs the GenGO algorithm.

Parameters:

[in] functionstoProcess Not Used

virtual void GenGOAlgorithm::computeEnrichmentForFunction	(	const string	funcType,
		const string	funcId
	)		`[inline, virtual]`

Computes whether one function is enriched.

Parameters:

[in]	type	a string specifying the type of the function.
[in]	functionId	a string specifying function.

void GenGOAlgorithm::printEnrichmentResults ( ostream & ostr ) [virtual]

prints the enrichment results

Parameters:

[in] ostr,an output stream to which the results will be written. Use cout for printing to a terminal.

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