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 EnrichmentAlgorithm
EnrichmentAlgorithm.EnrichmentAlgorithmType -
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final org.apfloat.Apfloatstatic final doubleFields inherited from class EnrichmentAlgorithmGreedy
adjustedPvalue, DEFAULT_MAX_PVALUE, maxPvalue, maxPvalueAjustedFields inherited from class EnrichmentAlgorithm
HTML_BG_COLOR, HTML_BG_COLOR_TITLE, HTML_TD_GENES_MAX_LEN, PRINT_SOMETHING_TIME -
Constructor Summary
ConstructorsConstructorDescriptionLeadingEdgeFractionAlgorithm(GeneSets geneSets, int numberToSelect, boolean orderDescending) -
Method Summary
Modifier and TypeMethodDescriptionvoidsetOrderDescending(boolean orderDescending) voidsetpValueCutOffQuantile(double pValueCutOffQuantile) Methods inherited from class EnrichmentAlgorithmGreedyVariableSize
greedyPvalue, setInitialSize, setSizeGrowthFactorMethods inherited from class EnrichmentAlgorithmGreedy
greedyPvalue, select, setAdjustedPvalue, setMaxGeneSetSize, setMaxPvalue, setMaxPvalueAjusted, setMinGeneSetSize, setVerbose, stopCriteriaMethods inherited from class 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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