Uses of Class
ubic.erminej.data.GeneSetResult

Packages that use GeneSetResult

Package	Description
ubic.erminej.analysis
ubic.erminej.data
ubic.erminej.gui.util

Uses of GeneSetResult in ubic.erminej.analysis

Methods in ubic.erminej.analysis that return GeneSetResult

Modifier and Type	Method and Description
protected GeneSetResult	OraPvalGenerator.classPval(Collection<Gene> genesAboveThresh, GeneSetTerm className) Get results for one class, based on class id.
GeneSetResult	CorrelationPvalGenerator.classPval(GeneSetTerm geneSetName)
GeneSetResult	GeneSetResamplingPvalGenerator.classPval(GeneSetTerm geneSetName) Get results for one class, based on class id.

Methods in ubic.erminej.analysis that return types with arguments of type GeneSetResult

Modifier and Type	Method and Description
Map<GeneSetTerm,GeneSetResult>	RocPvalGenerator.generateGeneSetResults()
Map<GeneSetTerm,GeneSetResult>	CorrelationPvalGenerator.generateGeneSetResults()
Map<GeneSetTerm,GeneSetResult>	OraPvalGenerator.generateGeneSetResults()
abstract Map<GeneSetTerm,GeneSetResult>	AbstractGeneSetPvalGenerator.generateGeneSetResults() Compute the results for all the gene sets under consideration.
Map<GeneSetTerm,GeneSetResult>	GeneSetResamplingPvalGenerator.generateGeneSetResults()
protected Map<GeneSetTerm,GeneSetResult>	RocPvalGenerator.generateGeneSetResults(boolean useMultifunctionalityCorrection)
protected Map<GeneSetTerm,GeneSetResult>	GeneSetResamplingPvalGenerator.generateGeneSetResults(boolean useMultifunctionalityCorrection)
Map<GeneSetTerm,GeneSetResult>	GeneSetPvalRun.getResults()

Method parameters in ubic.erminej.analysis with type arguments of type GeneSetResult

Modifier and Type	Method and Description
static List<GeneSetTerm>	GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results)
static List<GeneSetTerm>	GeneSetPvalRun.getSortedClasses(Map<GeneSetTerm,GeneSetResult> results, boolean useMfCorrection)
protected void	AbstractGeneSetPvalGenerator.multipleTestCorrect(List<GeneSetTerm> sortedClasses, Map<GeneSetTerm,GeneSetResult> results) Perform multiple test correction during the multifunctionality correction.
static List<GeneSetTerm>	GeneSetPvalRun.populateRanks(Map<GeneSetTerm,GeneSetResult> results) Fill in the ranks

Constructor parameters in ubic.erminej.analysis with type arguments of type GeneSetResult

Constructor and Description
GeneSetPvalRun(SettingsHolder settings, GeneAnnotations originalAnnots, StatusViewer messenger, Map<GeneSetTerm,GeneSetResult> results, String name) Use this when we are loading in existing results from a file.
MultipleTestCorrector(SettingsHolder set, List<GeneSetTerm> sc, GeneAnnotations geneData, GeneScores geneScores, Map<GeneSetTerm,GeneSetResult> results, StatusViewer messenger)

Uses of GeneSetResult in ubic.erminej.data

Subclasses of GeneSetResult in ubic.erminej.data

Modifier and Type	Class and Description
class	EmptyGeneSetResult Placeholder for sets that were not used.

Methods in ubic.erminej.data with parameters of type GeneSetResult

Modifier and Type	Method and Description
int	GeneSetResult.compareTo(GeneSetResult other) Default comparator for this class: sorts by the pvalue.
int	EmptyGeneSetResult.compareTo(GeneSetResult other)

Constructors in ubic.erminej.data with parameters of type GeneSetResult

Constructor and Description
GeneSetDetails(GeneSetTerm classID, GeneSetResult result, GeneAnnotations geneData, Settings settings, GeneScores geneScores, StatusViewer statusViewer) The data matrix will be read in based on the settings, or can be changed later.

Uses of GeneSetResult in ubic.erminej.gui.util

Methods in ubic.erminej.gui.util with parameters of type GeneSetResult

Modifier and Type	Method and Description
static Color	Colors.chooseColorForMultifunctionalityEffect(GeneSetResult value)