FunctionalEnrichmentAlgorithm Class Reference

This is an abstract algorithm for functional enrichment. More...

#include <enrichment-algorithm.h>

Inheritance diagram for FunctionalEnrichmentAlgorithm:

List of all members.

Public Member Functions
	FunctionalEnrichmentAlgorithm (const set< MyNodeId > &clusterGenes, const set< MyNodeId > &universeGenes, MyAnnotations &annotations, const GeneOntology &go, string category)
	Default constructor.
	FunctionalEnrichmentAlgorithm (MyAnnotations &annotations, const GeneOntology &go, string category)
	Constructor with only annotations.
virtual	~FunctionalEnrichmentAlgorithm ()
	Default destructor.
virtual void	computeEnrichedFunctions (const set< string > &functionsToProcess)
	Computes the enrichment of all the functions.
virtual void	computeEnrichmentForFunction (const string funcType, const string funcId)=0
	Computes whether one function is enriched.
virtual void	printEnrichmentResults (ostream &ostr)=0
	prints the enrichment results for each function.
Protected Attributes
set< MyNodeId >	_clusterGenes
	The set of genes in the cluster of interest.
set< MyNodeId >	_universeGenes
	The set of genes in the universe that we are considering.
MyAnnotations &	_annotations
	The annotations for the genes in _universeGenes.
const GeneOntology *	_go
	An instance of the gene ontology.
string	_category
	The category of genes for which we want to compute enrichment.
Static Protected Attributes
static LogHelper	_logHelper = LogHelper()
	Helper For computing factorial logs.

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Detailed Description

This is an abstract algorithm for functional enrichment.

This abstract base class simply serves as a skeleton to provide methods that different sub-classes must implement. Different sub-classes can have constructors with different signatures, depending on the arguments it needs. Note that this class and all subclasses assume that the cluster of interesting genes is a subset of the universe. This might not be checked and my lead to errors if the precondition doesn't hold.

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Constructor & Destructor Documentation

FunctionalEnrichmentAlgorithm::FunctionalEnrichmentAlgorithm	(	const set< MyNodeId > &	clusterGenes,
		const set< MyNodeId > &	universeGenes,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category
	)

Default constructor.

Parameters:

[in]	clusterGenes	A set of MyNodeIds that comprise the "cluster" we want to compute functional enrichment for.
[in]	universeGenes	A set of MyNodeIds that comprise the "universe" we are considering.
[in]	annotations	The set of functions and which genes they annotate.
[in]	go	An instance of the Gene Ontology.
[in]	category	The category of annotations on which to perform enrichment.

FunctionalEnrichmentAlgorithm::FunctionalEnrichmentAlgorithm	(	MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category
	)		[inline]

Constructor with only annotations.

We use this so subclasses can pass in only annotations if they want.

Parameters:

[in]	annotations	The set of functions and which genes they annotate.
[in]	go	An instance of the Gene Ontology.
[in]	category	The category of annotations on which to perform enrichment.

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Member Function Documentation

void FunctionalEnrichmentAlgorithm::computeEnrichedFunctions

(

const set< string > &

functionsToProcess

)

[virtual]

Computes the enrichment of all the functions.

Parameters:

[in]

functionstoProcess,a

set of strings, where each string represents a function ID. If the set is nonempty, functional enrichment will only be performed for the listed functions in this set.

Reimplemented in SetCoverEnrichment, FuncAssociate, EdgeGroupHyp, GroupHypAlgorithm, GenGOAlgorithm, RandomUniverseNetworkBasedEnrichmentAlgorithm, and RandomFunctionNetworkBasedEnrichmentAlgorithm.

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

Computes whether one function is enriched.

Parameters:

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

Implemented in SetCoverEnrichment, FuncAssociate, EdgeGroupHyp, GroupHypAlgorithm, GenGOAlgorithm, PAGEAlgorithm, HypergeometricAlgorithm, RandomUniverseNetworkBasedEnrichmentAlgorithm, and RandomFunctionNetworkBasedEnrichmentAlgorithm.

virtual void FunctionalEnrichmentAlgorithm::printEnrichmentResults

(

ostream &

ostr

)

[pure 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.

Implemented in SetCoverEnrichment, FuncAssociate, EdgeGroupHyp, GroupHypAlgorithm, GenGOAlgorithm, PAGEAlgorithm, HypergeometricAlgorithm, RandomUniverseNetworkBasedEnrichmentAlgorithm, and RandomFunctionNetworkBasedEnrichmentAlgorithm.

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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