Package org.snpeff.geneSets.algorithm
Class EnrichmentAlgorithmGreedy
- 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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- Direct Known Subclasses:
EnrichmentAlgorithmGreedyVariableSize
public abstract class EnrichmentAlgorithmGreedy extends EnrichmentAlgorithm
A generic greedy enrichment algorithm for selecting gene-sets- 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
Fields Modifier and Type Field Description protected boolean
adjustedPvalue
static double
DEFAULT_MAX_PVALUE
protected double
maxPvalue
protected double
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 EnrichmentAlgorithmGreedy(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)
Calculate best list of terms by adding a new term to a list that minimize p-value (rank sum)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 rangeResult
select()
Select the 'best' gene setsvoid
setAdjustedPvalue(boolean adjustedPvalue)
void
setMaxGeneSetSize(int maxGeneSetSize)
void
setMaxPvalue(double maxPvalue)
void
setMaxPvalueAjusted(double maxPvalueAjusted)
void
setMinGeneSetSize(int minGeneSetSize)
void
setVerbose(boolean verbose)
protected boolean
stopCriteria(Result result)
Stop criteria-
Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted
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Field Detail
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DEFAULT_MAX_PVALUE
public static final double DEFAULT_MAX_PVALUE
- See Also:
- Constant Field Values
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adjustedPvalue
protected boolean adjustedPvalue
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maxPvalue
protected double maxPvalue
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maxPvalueAjusted
protected double maxPvalueAjusted
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Constructor Detail
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EnrichmentAlgorithmGreedy
public EnrichmentAlgorithmGreedy(GeneSets geneSets, int numberToSelect)
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Method Detail
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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:
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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:
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select
public Result select()
Select the 'best' gene sets- Overrides:
select
in classEnrichmentAlgorithm
- Returns:
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setAdjustedPvalue
public void setAdjustedPvalue(boolean adjustedPvalue)
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setMaxGeneSetSize
public void setMaxGeneSetSize(int maxGeneSetSize)
- Overrides:
setMaxGeneSetSize
in classEnrichmentAlgorithm
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setMaxPvalue
public void setMaxPvalue(double maxPvalue)
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setMaxPvalueAjusted
public void setMaxPvalueAjusted(double maxPvalueAjusted)
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setMinGeneSetSize
public void setMinGeneSetSize(int minGeneSetSize)
- Overrides:
setMinGeneSetSize
in classEnrichmentAlgorithm
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setVerbose
public void setVerbose(boolean verbose)
- Overrides:
setVerbose
in classEnrichmentAlgorithm
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stopCriteria
protected boolean stopCriteria(Result result)
Stop criteria- Parameters:
result
-- Returns:
- true if stop criteria has been met and algorithm should stop iterating.
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