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

    Classes in org.snpeff.geneSets that implement interfaces with type arguments of type Result
    Modifier and Type
    Class
    Description
    class 
    Result
    Store a result form a greedy search algorithm
    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
    Modifier
    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