Package org.snpeff.geneSets.algorithm
Class LeadingEdgeFractionAlgorithm
- 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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- org.snpeff.geneSets.algorithm.FisherPValueGreedyAlgorithm
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- org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
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public class LeadingEdgeFractionAlgorithm extends FisherPValueGreedyAlgorithm
Leading edge fraction algorithm References: "Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits" http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001058 See page 12, "Step 4"- Author:
- pablocingolani
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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 static org.apfloat.Apfloat
ONE
static double
SCORE_CUTOFF_QUANTILE_DEFAULT
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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 LeadingEdgeFractionAlgorithm(GeneSets geneSets, int numberToSelect, boolean orderDescending)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
setOrderDescending(boolean orderDescending)
void
setpValueCutOffQuantile(double pValueCutOffQuantile)
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Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
greedyPvalue, setInitialSize, setSizeGrowthFactor
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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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Field Detail
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SCORE_CUTOFF_QUANTILE_DEFAULT
public static final double SCORE_CUTOFF_QUANTILE_DEFAULT
- See Also:
- Constant Field Values
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ONE
public static final org.apfloat.Apfloat ONE
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Constructor Detail
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LeadingEdgeFractionAlgorithm
public LeadingEdgeFractionAlgorithm(GeneSets geneSets, int numberToSelect, boolean orderDescending)
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