Package org.snpeff.geneSets.algorithm

Class EnrichmentAlgorithmGreedy

java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
Direct Known Subclasses:
EnrichmentAlgorithmGreedyVariableSize
public abstract class EnrichmentAlgorithmGreedy extends EnrichmentAlgorithm
A generic greedy enrichment algorithm for selecting gene-sets
Author:
pcingola

  • Field Details

    • DEFAULT_MAX_PVALUE

      public static final double DEFAULT_MAX_PVALUE
      See Also:

    • adjustedPvalue

      protected boolean adjustedPvalue

    • maxPvalue

      protected double maxPvalue

    • maxPvalueAjusted

      protected double maxPvalueAjusted

  • Constructor Details

    • EnrichmentAlgorithmGreedy

      public EnrichmentAlgorithmGreedy(GeneSets geneSets, int numberToSelect)

  • Method Details

    • greedyPvalue

      protected Result greedyPvalue(Result prevResult)
      Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)
      Returns:

    • greedyPvalue

      protected Result 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
      Returns:

    • select

      public Result select()
      Select the 'best' gene sets
      Overrides:
      select in class EnrichmentAlgorithm
      Returns:

    • setAdjustedPvalue

      public void setAdjustedPvalue(boolean adjustedPvalue)

    • setMaxGeneSetSize

      public void setMaxGeneSetSize(int maxGeneSetSize)
      Overrides:
      setMaxGeneSetSize in class EnrichmentAlgorithm

    • setMaxPvalue

      public void setMaxPvalue(double maxPvalue)

    • setMaxPvalueAjusted

      public void setMaxPvalueAjusted(double maxPvalueAjusted)

    • setMinGeneSetSize

      public void setMinGeneSetSize(int minGeneSetSize)
      Overrides:
      setMinGeneSetSize in class EnrichmentAlgorithm

    • setVerbose

      public void setVerbose(boolean verbose)
      Overrides:
      setVerbose in class EnrichmentAlgorithm

    • stopCriteria

      protected boolean stopCriteria(Result result)
      Stop criteria
      Parameters:
      result -
      Returns:
      true if stop criteria has been met and algorithm should stop iterating.