Package org.snpeff.geneSets.algorithm
Class EnrichmentAlgorithm
java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
- Direct Known Subclasses:
EnrichmentAlgorithmGreedy
,FisherPValueAlgorithm
,NoneAlgorithm
,RankSumPValueAlgorithm
A generic enrichment algorithm for selecting gene-sets from a collection of gene-sets
- Author:
- pcingola
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Nested Class Summary
Nested Classes -
Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiondouble
protected boolean
Showld we show this result or should the output be filtered?protected void
select()
Select the 'best' gene setsvoid
setDebug
(boolean debug) void
setFilterOutputGeneSets
(Set<String> filterOutputGeneSets) void
setHtmlTable
(boolean htmlTable) void
setMaxGeneSetSize
(int maxGeneSetSize) void
setMaxPValue
(double maxPValue) void
setMaxPvalueAdjusted
(double maxPvalueAdjusted) void
setMinGeneSetSize
(int minGeneSetSize) void
setVerbose
(boolean verbose)
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Field Details
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HTML_TD_GENES_MAX_LEN
public static final int HTML_TD_GENES_MAX_LEN- See Also:
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HTML_BG_COLOR
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HTML_BG_COLOR_TITLE
- See Also:
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PRINT_SOMETHING_TIME
public static long PRINT_SOMETHING_TIME
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Constructor Details
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EnrichmentAlgorithm
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Method Details
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getMaxPvalueAdjusted
public double getMaxPvalueAdjusted() -
getOutput
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isShow
Showld we show this result or should the output be filtered?- Parameters:
result
-- Returns:
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print
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select
Select the 'best' gene sets- Returns:
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setDebug
public void setDebug(boolean debug) -
setFilterOutputGeneSets
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setHtmlTable
public void setHtmlTable(boolean htmlTable) -
setMaxGeneSetSize
public void setMaxGeneSetSize(int maxGeneSetSize) -
setMaxPValue
public void setMaxPValue(double maxPValue) -
setMaxPvalueAdjusted
public void setMaxPvalueAdjusted(double maxPvalueAdjusted) -
setMinGeneSetSize
public void setMinGeneSetSize(int minGeneSetSize) -
setVerbose
public void setVerbose(boolean verbose)
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