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