RankSumPValueGreedyAlgorithm (SnpEff 5.4 API)

java.lang.Object

org.snpeff.geneSets.algorithm.EnrichmentAlgorithm

org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy

org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize

org.snpeff.geneSets.algorithm.RankSumPValueGreedyAlgorithm

public class RankSumPValueGreedyAlgorithm extends EnrichmentAlgorithmGreedyVariableSize

Nested Class Summary

Nested classes/interfaces inherited from class EnrichmentAlgorithm
EnrichmentAlgorithm.EnrichmentAlgorithmType
Field Summary

Fields inherited from class EnrichmentAlgorithmGreedy
adjustedPvalue, DEFAULT_MAX_PVALUE, maxPvalue, maxPvalueAjusted

Fields inherited from class EnrichmentAlgorithm
HTML_BG_COLOR, HTML_BG_COLOR_TITLE, HTML_TD_GENES_MAX_LEN, PRINT_SOMETHING_TIME
Constructor Summary

Constructors

Constructor

Description

RankSumPValueGreedyAlgorithm(GeneSetsRanked geneSets, int numberToSelect)
Method Summary

Modifier and Type

Method

Description

protected boolean

stopCriteria(Result result)

Stop criteria

Methods inherited from class EnrichmentAlgorithmGreedyVariableSize
greedyPvalue, setInitialSize, setSizeGrowthFactor

Methods inherited from class EnrichmentAlgorithmGreedy
greedyPvalue, select, setAdjustedPvalue, setMaxGeneSetSize, setMaxPvalue, setMaxPvalueAjusted, setMinGeneSetSize, setVerbose

Methods inherited from class EnrichmentAlgorithm
getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- RankSumPValueGreedyAlgorithm
  
  public RankSumPValueGreedyAlgorithm(GeneSetsRanked geneSets, int numberToSelect)
Method Details
- stopCriteria
  
  protected boolean stopCriteria(Result result)
  
  Stop criteria
  
  Overrides:
  
  stopCriteria in class EnrichmentAlgorithmGreedy
  
  Parameters:
  
  result -
  
  Returns: