Uses of Class
org.snpeff.geneSets.Result

Packages that use Result

Package	Description
org.snpeff.geneSets
org.snpeff.geneSets.algorithm

Uses of Result in org.snpeff.geneSets

Methods in org.snpeff.geneSets with parameters of type Result

Modifier and Type	Method	Description
int	Result.compareTo(Result res)

Constructors in org.snpeff.geneSets with parameters of type Result

Constructor	Description
Result(Result res)

Uses of Result in org.snpeff.geneSets.algorithm

Methods in org.snpeff.geneSets.algorithm that return Result

Modifier and Type	Method	Description
protected 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 range
protected Result	EnrichmentAlgorithmGreedyVariableSize.greedyPvalue(Result prevResult)	Find best p-value using a greedy algorithm (smaller gene sets first)
Result	EnrichmentAlgorithm.select()	Select the 'best' gene sets
Result	EnrichmentAlgorithmGreedy.select()	Select the 'best' gene sets

Methods in org.snpeff.geneSets.algorithm with parameters of type Result

Modifier and Type	Method	Description
protected 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 range
protected Result	EnrichmentAlgorithmGreedyVariableSize.greedyPvalue(Result prevResult)	Find best p-value using a greedy algorithm (smaller gene sets first)
protected boolean	EnrichmentAlgorithm.isShow(Result result)	Showld we show this result or should the output be filtered?
protected boolean	EnrichmentAlgorithmGreedy.stopCriteria(Result result)	Stop criteria
protected boolean	RankSumPValueGreedyAlgorithm.stopCriteria(Result result)	Stop criteria