SetCoverEnrichment Class Reference

This class implements an enrichment algorithm based on set cover. More...

#include <enrichment-algorithm.h>

Inheritance diagram for SetCoverEnrichment:

List of all members.

Classes
struct	FuncStats
Public Member Functions
	SetCoverEnrichment (const MyGraph &clusterGraph, const MyGraph &universeGraph, MyAnnotations &annotations, const GeneOntology &go, string category)
	Default constructor.
virtual	~SetCoverEnrichment ()
	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)
	not used
virtual void	printEnrichmentResults (ostream &ostr)
	prints the enrichment results for each function.

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Detailed Description

This class implements an enrichment algorithm based on set cover.

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Constructor & Destructor Documentation

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

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.

Warning:

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

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Member Function Documentation

void SetCoverEnrichment::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 from FunctionalEnrichmentAlgorithm.

void SetCoverEnrichment::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