Package org.snpeff.geneSets.algorithm
Class EnrichmentAlgorithmGreedyVariableSize
- java.lang.Object
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- org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
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- org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
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- org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
EnrichmentAlgorithm.EnrichmentAlgorithmType
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Field Summary
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Fields inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
adjustedPvalue, DEFAULT_MAX_PVALUE, maxPvalue, maxPvalueAjusted
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Fields inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
HTML_BG_COLOR, HTML_BG_COLOR_TITLE, HTML_TD_GENES_MAX_LEN, PRINT_SOMETHING_TIME
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Constructor Summary
Constructors Constructor Description EnrichmentAlgorithmGreedyVariableSize(GeneSets geneSets, int numberToSelect)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected Result
greedyPvalue(Result prevResult)
Find best p-value using a greedy algorithm (smaller gene sets first)void
setInitialSize(int initialSize)
void
setSizeGrowthFactor(int sizeGrowthFactor)
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Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
greedyPvalue, select, setAdjustedPvalue, setMaxGeneSetSize, setMaxPvalue, setMaxPvalueAjusted, setMinGeneSetSize, setVerbose, stopCriteria
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Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted
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Constructor Detail
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EnrichmentAlgorithmGreedyVariableSize
public EnrichmentAlgorithmGreedyVariableSize(GeneSets geneSets, int numberToSelect)
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Method Detail
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greedyPvalue
protected Result greedyPvalue(Result prevResult)
Find best p-value using a greedy algorithm (smaller gene sets first)- Overrides:
greedyPvalue
in classEnrichmentAlgorithmGreedy
- Returns:
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setInitialSize
public void setInitialSize(int initialSize)
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setSizeGrowthFactor
public void setSizeGrowthFactor(int sizeGrowthFactor)
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