Package org.snpeff.geneSets.algorithm

Class EnrichmentAlgorithmGreedyVariableSize

java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
Direct Known Subclasses:
FisherPValueGreedyAlgorithm, RankSumPValueGreedyAlgorithm
public abstract class EnrichmentAlgorithmGreedyVariableSize extends EnrichmentAlgorithmGreedy
A greedy enrichment algorithm for selecting gene-sets using a variable geneSet-size strategy: i) Select only from geneSets in low-sizes e.g. geneSet.size() in [1-10] ii) If p-value goes up, use a larger geneSize range, e.g. geneSet.size() in [11-20]
Author:
pcingola

  • Constructor Details

    • EnrichmentAlgorithmGreedyVariableSize

      public EnrichmentAlgorithmGreedyVariableSize(GeneSets geneSets, int numberToSelect)

  • Method Details

    • greedyPvalue

      protected Result greedyPvalue(Result prevResult)
      Find best p-value using a greedy algorithm (smaller gene sets first)
      Overrides:
      greedyPvalue in class EnrichmentAlgorithmGreedy
      Returns:

    • setInitialSize

      public void setInitialSize(int initialSize)

    • setSizeGrowthFactor

      public void setSizeGrowthFactor(int sizeGrowthFactor)