Package org.snpeff.geneSets.algorithm
Class LeadingEdgeFractionAlgorithm
java.lang.Object
org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedy
org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
org.snpeff.geneSets.algorithm.FisherPValueGreedyAlgorithm
org.snpeff.geneSets.algorithm.LeadingEdgeFractionAlgorithm
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
Nested classes/interfaces inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithm
EnrichmentAlgorithm.EnrichmentAlgorithmType
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final org.apfloat.Apfloat
static final double
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
ConstructorsConstructorDescriptionLeadingEdgeFractionAlgorithm
(GeneSets geneSets, int numberToSelect, boolean orderDescending) -
Method Summary
Modifier and TypeMethodDescriptionvoid
setOrderDescending
(boolean orderDescending) void
setpValueCutOffQuantile
(double pValueCutOffQuantile) Methods inherited from class org.snpeff.geneSets.algorithm.EnrichmentAlgorithmGreedyVariableSize
greedyPvalue, setInitialSize, setSizeGrowthFactor
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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Field Details
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SCORE_CUTOFF_QUANTILE_DEFAULT
public static final double SCORE_CUTOFF_QUANTILE_DEFAULT- See Also:
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ONE
public static final org.apfloat.Apfloat ONE
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Constructor Details
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LeadingEdgeFractionAlgorithm
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Method Details
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setOrderDescending
public void setOrderDescending(boolean orderDescending) -
setpValueCutOffQuantile
public void setpValueCutOffQuantile(double pValueCutOffQuantile)
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