Collaboration diagram for broad.projection.gsa.GeneSetEnrichment:

Public Member Functions
	GeneSetEnrichment (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, Map< String, Collection< String >> geneSets, boolean normalizeScores, boolean permutePhenotype)

	GeneSetEnrichment (MatrixWithHeaders data, Collection< String > group1, Collection< String > group2, Map< String, Collection< String >> geneSets)

	GeneSetEnrichment (MatrixWithHeaders patternData, MatrixWithHeaders geneData, Map< String, Collection< String >> geneSets, boolean normalizeScores, boolean permutePhenotype)

MatrixWithHeaders	getRankedList ()

MatrixWithHeaders	getKSFDR ()

MatrixWithHeaders	getMaxMeanFDR ()

MatrixWithHeaders	getMaxMeanEnrichments ()

MatrixWithHeaders	getKSEnrichments ()

MatrixWithHeaders	getNormalizedKSEnrichments ()

MatrixWithHeaders	getNormalizedMaxMeanEnrichments ()

Constructor & Destructor Documentation

broad.projection.gsa.GeneSetEnrichment.GeneSetEnrichment	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		Map< String, Collection< String >>	geneSets,
		boolean	normalizeScores,
		boolean	permutePhenotype
	)

broad.projection.gsa.GeneSetEnrichment.GeneSetEnrichment	(	MatrixWithHeaders	data,
		Collection< String >	group1,
		Collection< String >	group2,
		Map< String, Collection< String >>	geneSets
	)

broad.projection.gsa.GeneSetEnrichment.GeneSetEnrichment	(	MatrixWithHeaders	patternData,
		MatrixWithHeaders	geneData,
		Map< String, Collection< String >>	geneSets,
		boolean	normalizeScores,
		boolean	permutePhenotype
	)

Member Function Documentation

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getKSEnrichments ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getKSFDR ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getMaxMeanEnrichments ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getMaxMeanFDR ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getNormalizedKSEnrichments ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getNormalizedMaxMeanEnrichments ( )

MatrixWithHeaders broad.projection.gsa.GeneSetEnrichment.getRankedList ( )

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