Uses of Class
org.snpeff.geneSets.Result
Packages that use Result
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Uses of Result in org.snpeff.geneSets
Methods in org.snpeff.geneSets with parameters of type ResultConstructors in org.snpeff.geneSets with parameters of type Result -
Uses of Result in org.snpeff.geneSets.algorithm
Methods in org.snpeff.geneSets.algorithm that return ResultModifier and TypeMethodDescriptionprotected Result
EnrichmentAlgorithmGreedy.greedyPvalue
(Result prevResult) Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)protected Result
EnrichmentAlgorithmGreedy.greedyPvalue
(Result prevResult, int minGeneSetSize, int maxGeneSetSize) Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size rangeprotected Result
EnrichmentAlgorithmGreedyVariableSize.greedyPvalue
(Result prevResult) Find best p-value using a greedy algorithm (smaller gene sets first)EnrichmentAlgorithm.select()
Select the 'best' gene setsEnrichmentAlgorithmGreedy.select()
Select the 'best' gene setsMethods in org.snpeff.geneSets.algorithm with parameters of type ResultModifier and TypeMethodDescriptionprotected Result
EnrichmentAlgorithmGreedy.greedyPvalue
(Result prevResult) Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)protected Result
EnrichmentAlgorithmGreedy.greedyPvalue
(Result prevResult, int minGeneSetSize, int maxGeneSetSize) Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum) Only look for genesets within [minGeneSetSize, maxGeneSetSize] size rangeprotected Result
EnrichmentAlgorithmGreedyVariableSize.greedyPvalue
(Result prevResult) Find best p-value using a greedy algorithm (smaller gene sets first)protected boolean
Showld we show this result or should the output be filtered?protected boolean
EnrichmentAlgorithmGreedy.stopCriteria
(Result result) Stop criteriaprotected boolean
RankSumPValueGreedyAlgorithm.stopCriteria
(Result result) Stop criteria