This class implements the Parametric Analysis of Gene Set Enrichment (PAGE) algorithm by Kim and Volsky, BMC Bioinformatics 2005: http://www.biomedcentral.com/1471-2105/6/144. More...

Inheritance diagram for PAGEAlgorithm:

Classes
struct	enrichmentResult
Public Member Functions
	PAGEAlgorithm (const MyPointSet &universePoints, MyAnnotations &annotations, const GeneOntology &go, string category)
	Constructor.
virtual	~PAGEAlgorithm ()
	Default destructor.
virtual void	computeEnrichmentForFunction (const string funcType, const string funcId)
	Computes the enrichhment score for teh given function.
virtual void	printEnrichmentResults (ostream &ostr)
	prints the enrichment results for each function.

Detailed Description

This class implements the Parametric Analysis of Gene Set Enrichment (PAGE) algorithm by Kim and Volsky, BMC Bioinformatics 2005: http://www.biomedcentral.com/1471-2105/6/144.

Constructor & Destructor Documentation

PAGEAlgorithm::PAGEAlgorithm	(	const MyPointSet &	universePoints,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category
	)

Constructor.

Parameters:

[in]	universePoints	The gene expression values, one sample per dimension.
[in]	annotations	The annotations for the genes.
[in]	go	An instance of the GeneOntology.
[in]	category	The annotations category to test for enrichment.

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

Computes the enrichhment score for teh given function.

Parameters:

[in]	funcType	The type of the function that is being tested for enrichment.
[in]	funcId	The ID of the function to test for enrichment.

void PAGEAlgorithm::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.

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