HypergeometricAlgorithm Class Reference

This class implements the set-based hypergeometric algorithm for computing functional enrichment. More...

#include <enrichment-algorithm.h>

Inheritance diagram for HypergeometricAlgorithm:

List of all members.

Classes
struct	hypergeometricEnrichmentResult
	This structure stores various enrichment results calculated during functional enrichment. Any p-values that are computed will be stored in this structure along with their associated function. More...
Public Member Functions
	HypergeometricAlgorithm (const set< string > &clusterGraph, const set< string > &universeSet, MyAnnotations &annotations, const GeneOntology &go, string category)
	Constructor.
	HypergeometricAlgorithm (const MyGraph &clusterGraph, const MyGraph &universeGraph, MyAnnotations &annotations, const GeneOntology &go, string category)
	Constructor.
virtual	~HypergeometricAlgorithm ()
	Default destructor.
virtual void	computeEnrichmentForFunction (const string funcType, const string funcId)
	Determines the sizes of the 4 sets needed to calculate the hyergeometric p-value: universe size, cluster size, function size, cluster-and-function size.
virtual void	printEnrichmentResults (ostream &ostr)
	prints the enrichment results for each function.
Static Public Member Functions
static long double	getHypergeometricPvalue (int v, int c, int v_f, int c_f)
	calculates Fisher's one-sided exact test for the given values. This sums the following over all values of k, where c_f <= k <= min(v_f, c): choose(c,k)*choose(v-c,v_f-k)/choose(v, v_f)

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Detailed Description

This class implements the set-based hypergeometric algorithm for computing functional enrichment.

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Constructor & Destructor Documentation

HypergeometricAlgorithm::HypergeometricAlgorithm	(	const set< string > &	clusterGraph,
		const set< string > &	universeSet,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category
	)

Constructor.

Parameters:

[in]	clusterSet	is a set of strings storing the "cluster" for which we want to compute functional enrichment.
[in]	universeSet	a set of strings storing the universe of genes.
[in]	annotations	The annotations for the genes.

Warning:

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

HypergeometricAlgorithm::HypergeometricAlgorithm	(	const MyGraph &	clusterGraph,
		const MyGraph &	universeGraph,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category
	)

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.

Warning:

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

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Member Function Documentation

void HypergeometricAlgorithm::computeEnrichmentForFunction	(	const string	funcType,
		const string	funcId
	)		[virtual]

Determines the sizes of the 4 sets needed to calculate the hyergeometric p-value: universe size, cluster size, function size, cluster-and-function size.

Parameters:

[in]

Implements FunctionalEnrichmentAlgorithm.

long double HypergeometricAlgorithm::getHypergeometricPvalue	(	int	v,
		int	c,
		int	v_f,
		int	c_f
	)		[static]

calculates Fisher's one-sided exact test for the given values. This sums the following over all values of k, where c_f <= k <= min(v_f, c): choose(c,k)*choose(v-c,v_f-k)/choose(v, v_f)

Parameters:

[in]	v,the	size of the universe set V
[in]	c,the	size of the "cluster" set C
[in]	v_f,the	size of the set of elements in V annotated with function f.
[in]	c_f,the	size of the set of elements in C annotated with function f.

void HypergeometricAlgorithm::printEnrichmentResults

(

ostream &

ostr

)

[virtual]

prints the enrichment results for each function.

Parameters:

[in]

ostr,an

output stream to which the results will be written. Use cout for printing to a terminal.

Implements FunctionalEnrichmentAlgorithm.

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

• /home/poirel/src/c++/biorithm/libfun/enrichment-algorithm.h
• /home/poirel/src/c++/biorithm/libfun/enrichment-algorithm.C