Package org.snpeff.stats
Class ObservedOverExpected
java.lang.Object
org.snpeff.stats.ObservedOverExpected
- Direct Known Subclasses:
ObservedOverExpectedCHG
,ObservedOverExpectedCHH
,ObservedOverExpectedCpG
Observed over expected values (o/e) ratios
E.g.: CpG dinucleotides in a sequence
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionabstract double
double
Expected number of sequences (average between plus and minus strand)double
Expected number of sequences (average between plus and minus strand)double
Expected number of sequences (average between plus and minus strand)abstract int
int
Observed sequence (average between plus and minus strand)int
Observed sequence (average between plus and minus strand)int
Observed sequence (average between plus and minus strand)int
observedChg
(String sequence) Count the number of CHG in this sequencedouble
Observed over expected ratiodouble
Observed over expected ratiodouble
Observed over expected ratiodouble
oe
(Transcript t) Observed over expected ratio
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Constructor Details
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ObservedOverExpected
public ObservedOverExpected()
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Method Details
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expected
Expected number of sequences (average between plus and minus strand)- Parameters:
e
- : Exon- Returns:
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expected
Expected number of sequences (average between plus and minus strand)- Parameters:
t
- : Transcript- Returns:
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expected
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expected
Expected number of sequences (average between plus and minus strand)- Parameters:
t
- : Transcript- Returns:
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observed
Observed sequence (average between plus and minus strand)- Parameters:
e
- : Exon- Returns:
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observed
Observed sequence (average between plus and minus strand)- Parameters:
g
- : Gene- Returns:
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observed
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observed
Observed sequence (average between plus and minus strand)- Parameters:
t
- : Transcript- Returns:
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observedChg
Count the number of CHG in this sequence- Parameters:
sequence
-- Returns:
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oe
Observed over expected ratio- Parameters:
Exon
-- Returns:
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oe
Observed over expected ratio- Parameters:
Gene
-- Returns:
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oe
Observed over expected ratio- Parameters:
sequence
-- Returns:
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oe
Observed over expected ratio- Parameters:
Transcript
-- Returns:
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