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
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
Nested classes/interfaces inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
EnrichmentAlgorithm.EnrichmentAlgorithmType
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Field Summary
Fields inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
adjustedPvalue, DEFAULT_MAX_PVALUE, maxPvalue, maxPvalueAjusted
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
ConstructorsConstructorDescriptionEnrichmentAlgorithmGreedyVariableSize
(GeneSets geneSets, int numberToSelect) -
Method Summary
Modifier and TypeMethodDescriptionprotected Result
greedyPvalue
(Result prevResult) Find best p-value using a greedy algorithm (smaller gene sets first)void
setInitialSize
(int initialSize) void
setSizeGrowthFactor
(int sizeGrowthFactor) Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
greedyPvalue, select, setAdjustedPvalue, setMaxGeneSetSize, setMaxPvalue, setMaxPvalueAjusted, setMinGeneSetSize, setVerbose, stopCriteria
Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted
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Constructor Details
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EnrichmentAlgorithmGreedyVariableSize
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Method Details
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greedyPvalue
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) -
setSizeGrowthFactor
public void setSizeGrowthFactor(int sizeGrowthFactor)
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