Package org.snpeff.stats
Class VariantEffectStats
java.lang.Object
org.snpeff.stats.VariantEffectStats
- All Implemented Interfaces:
SamplingStats<VariantEffect>
Variants annotation statistics.
These are statistics about each variant annotation / effect. There can be
multiple annotaitons per variant (e.g. multiple transcripts in a gene
produce multiple annotations in a single variant).
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Field Summary
Fields -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAaChangeColor
(String oldAa, String newAa) Background color used for AA change tablelong
getAaChangeCount
(String oldAa, String newAa) How many changes from oldAa to newAa do we have?Get list of all amino acisd involvedgetCodonChangeColor
(String oldCodon, String newCodon) long
getCodonChangeCount
(String oldCodon, String newCodon) How many changes from oldCodo to newCodon do we have?Get a list of all codons involvedint
int
Barplot of different gene regionsdouble
boolean
hasData()
Does this statistic have any data?void
sample
(VariantEffect variantEffect) Analyze one samplevoid
setUseSequenceOntology
(boolean useSequenceOntology)
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Field Details
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CHANGE_SEPARATOR
- See Also:
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Constructor Details
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VariantEffectStats
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Method Details
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getAaChangeColor
Background color used for AA change table -
getAaChangeCount
How many changes from oldAa to newAa do we have? -
getAaList
Get list of all amino acisd involved -
getCodonChangeColor
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getCodonChangeCount
How many changes from oldCodo to newCodon do we have? -
getCodonList
Get a list of all codons involved -
getCountByEffect
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getCountByFunctionalClass
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getCountByGeneRegion
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getCountByImpact
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getCountErrors
public int getCountErrors() -
getCountWarnings
public int getCountWarnings() -
getGeneCountByEffectTable
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getGeneCountByImpactTable
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getGeneCountByRegionTable
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getPlotGene
Barplot of different gene regions -
getSilentRatio
public double getSilentRatio() -
hasData
public boolean hasData()Description copied from interface:SamplingStats
Does this statistic have any data?- Specified by:
hasData
in interfaceSamplingStats<VariantEffect>
- Returns:
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sample
Description copied from interface:SamplingStats
Analyze one sample- Specified by:
sample
in interfaceSamplingStats<VariantEffect>
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setUseSequenceOntology
public void setUseSequenceOntology(boolean useSequenceOntology)
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