RandomFunctionNetworkBasedEnrichmentAlgorithm Class Reference

Calculates enrichment based on network connectivity using various randomization techniques by randomly selecting sets X, where the size of X is the number of nodes annotated with function f. This is repeated for each function. More...

#include <enrichment-algorithm.h>

Inheritance diagram for RandomFunctionNetworkBasedEnrichmentAlgorithm:

List of all members.

Classes
struct	randomFunctionEnrichmentResult
	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.
Public Member Functions
	RandomFunctionNetworkBasedEnrichmentAlgorithm (const MyGraph &clusterGraph, const MyGraph &universeGraph, MyAnnotations &annotations, const GeneOntology &go, string category, unsigned int numRandomGraphs)
	Default constructor.
virtual	~RandomFunctionNetworkBasedEnrichmentAlgorithm ()
	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)
	Computes whether one function is enriched.
void	printEnrichmentResult (ostream &ostr, randomFunctionEnrichmentResult result)
	Prints functional enrichment information for a single function.
virtual void	printEnrichmentResults (ostream &ostr)
	prints the enrichment results for each function.

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Detailed Description

Calculates enrichment based on network connectivity using various randomization techniques by randomly selecting sets X, where the size of X is the number of nodes annotated with function f. This is repeated for each function.

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Constructor & Destructor Documentation

RandomFunctionNetworkBasedEnrichmentAlgorithm::RandomFunctionNetworkBasedEnrichmentAlgorithm	(	const MyGraph &	clusterGraph,
		const MyGraph &	universeGraph,
		MyAnnotations &	annotations,
		const GeneOntology &	go,
		string	category,
		unsigned int	numRandomGraphs
	)

Default constructor.

Parameters:

[in]	clusterGraph	an instance of MyGraph storing the "cluster" we want to compute functional enrichment for.
[in]	universeGraph	an instance of MyGraph storing the universe of genes.
[in]	annotations	The annotations for the genes.
[in]	go	an instance of the Gene Ontology DAG

Warning:

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

Parameters:

[in]	numRandomGraphs	an integer specifying how many random graphs to produce.
[in]	numRandomizationIterations	an integer specifying how many iterations to run the randomization algorithm to produce a single random graph.

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Member Function Documentation

void RandomFunctionNetworkBasedEnrichmentAlgorithm::computeEnrichmentForFunction	(	const string	funcType,
		const string	funcId
	)		[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 RandomFunctionNetworkBasedEnrichmentAlgorithm::printEnrichmentResult	(	ostream &	ostr,
		randomFunctionEnrichmentResult	result
	)

Prints functional enrichment information for a single function.

Parameters:

[in]	ostream,an	output stream to which the results will be written.
[in]	enrichmentResult	an instance of the enrichment result structure to print.

void RandomFunctionNetworkBasedEnrichmentAlgorithm::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