Package org.snpeff.geneSets.algorithm
Class EnrichmentAlgorithmGreedy
java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
- Direct Known Subclasses:
EnrichmentAlgorithmGreedyVariableSize
A generic greedy enrichment algorithm for selecting gene-sets
- 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
FieldsModifier and TypeFieldDescriptionprotected boolean
static final double
protected double
protected double
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 -
Method Summary
Modifier and TypeMethodDescriptionprotected 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 rangeselect()
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 criteriaMethods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
getMaxPvalueAdjusted, getOutput, isShow, print, setDebug, setFilterOutputGeneSets, setHtmlTable, setMaxPValue, setMaxPvalueAdjusted
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Field Details
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DEFAULT_MAX_PVALUE
public static final double DEFAULT_MAX_PVALUE- See Also:
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adjustedPvalue
protected boolean adjustedPvalue -
maxPvalue
protected double maxPvalue -
maxPvalueAjusted
protected double maxPvalueAjusted
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Constructor Details
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EnrichmentAlgorithmGreedy
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Method Details
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greedyPvalue
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
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
Select the 'best' gene sets- Overrides:
select
in classEnrichmentAlgorithm
- Returns:
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setAdjustedPvalue
public void setAdjustedPvalue(boolean adjustedPvalue) -
setMaxGeneSetSize
public void setMaxGeneSetSize(int maxGeneSetSize) - Overrides:
setMaxGeneSetSize
in classEnrichmentAlgorithm
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setMaxPvalue
public void setMaxPvalue(double maxPvalue) -
setMaxPvalueAjusted
public void setMaxPvalueAjusted(double maxPvalueAjusted) -
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
Stop criteria- Parameters:
result
-- Returns:
- true if stop criteria has been met and algorithm should stop iterating.
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