FuncAssociate Class Reference

This class implements the FuncAssociate enrichment method: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/18/2502. More...

#include <enrichment-algorithm.h>

Inheritance diagram for FuncAssociate:

List of all members.

Classes
struct	FunctionInfo
	information about a function.
Public Member Functions
	FuncAssociate (const MyPointSet &clusterPoints, const set< string > &universeSet, MyAnnotations &annotations, const GeneOntology &go, string category, string outfile)
	Default constructor.
virtual	~FuncAssociate ()
	Default destructor.
virtual void	computeEnrichedFunctions (const set< string > &functionsToProcess)
	Computes functional enrichment using the FuncAssociate 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

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Detailed Description

This class implements the FuncAssociate enrichment method: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/18/2502.

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Constructor & Destructor Documentation

FuncAssociate::FuncAssociate	(	const MyPointSet &	clusterPoints,
		const set< string > &	universeSet,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category,
		string	outfile
	)

Default constructor.

Parameters:

[in]	clusterPoints	The cluster on which we want to perform enrichment.
[in]	universeSet	The universe of genes.
[in]	annotations	The annotations for the genes.
[in]	go	An instance of the Gene Ontology.
[in]	category	A string indicating the category of functions on which to perform enrichment. An empty string indicates all categories.
[in]	rankedGenes	A list of ranked genes, where the lowest index indicates the most importan (i.e., highest ranked) gene.

Warning:

The set of genes in rankedGenes should be a subset of the genes in universeGraph, but this condition is not checked.

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Member Function Documentation

void FuncAssociate::computeEnrichedFunctions

(

const set< string > &

functionsToProcess

)

[virtual]

Computes functional enrichment using the FuncAssociate algorithm.

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.

virtual void FuncAssociate::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.

Implements FunctionalEnrichmentAlgorithm.

void FuncAssociate::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.

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