Package org.snpsift.hwe
Class VcfHwe
- java.lang.Object
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- org.snpsift.hwe.VcfHwe
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public class VcfHwe extends java.lang.Object
Calculate Hardy-Weimberg equilibrium and goodness of fit. References: "Principles of population genetics", Hartl & Clark "A Note on Exact test of Hardy Weinbeg Equilibrium", G. Abecasis et. al. Note: This is only for two alleles in diploid individuals. We should extend this to more alleles and N-ploid species.- Author:
- pablocingolani
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Field Summary
Fields Modifier and Type Field Description static boolean
debug
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Constructor Summary
Constructors Constructor Description VcfHwe()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
hwe(org.snpeff.vcf.VcfEntry vcfEntry, boolean addInfo)
Calculate Hardy-Weimberg equilibrium and add data to vcfEntry (INFO fields)double
hweLogPn12(int n1, int n2, int n12)
Calculate exact log of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl & Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.double
hweP(int n1, int n2, int n12star)
Calculate goodness of fit for n1, n2 combination.double
hwePchi2(int n1, int n2, int n12)
Calculate goodness of fit using Chi square approximationdouble
hwePn12(int n1, int n2, int n12)
Calculate exact probability of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl & Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G.
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Method Detail
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hwe
public double hwe(org.snpeff.vcf.VcfEntry vcfEntry, boolean addInfo)
Calculate Hardy-Weimberg equilibrium and add data to vcfEntry (INFO fields)- Parameters:
addInfo
- : If true, 'HWE' and 'HWEP' INFO tags are added to this entry
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hweLogPn12
public double hweLogPn12(int n1, int n2, int n12)
Calculate exact log of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl & Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G. Abecasis et. al. (formula 1)- Parameters:
n1
- : Number of 'A' allelesn2
- : Number of 'B' allelesn12
- : Number of 'AB' individuals Note: Total number of individuals (assuming they are diploid) is N = (n1 + n2) / 2- Returns:
- Log of pValue using exact test
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hweP
public double hweP(int n1, int n2, int n12star)
Calculate goodness of fit for n1, n2 combination. References: "Principles of population genetics", Hartl & Clark, page 58 WARNING: The formula P_{HWE} in page 2 of "A Note on Exact test of Hardy Weinbeg Equilibrium", seems to have two mistakes (probably typos?)
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hwePchi2
public double hwePchi2(int n1, int n2, int n12)
Calculate goodness of fit using Chi square approximation
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hwePn12
public double hwePn12(int n1, int n2, int n12)
Calculate exact probability of "P[ n12 | n1, n2]" References: "Principles of population genetics", Hartl & Clark, page 58 (formula 2.5) "A Note on Exact test of Hardy Weinbeg Equilibrium", G. Abecasis et. al. (formula 1)- Parameters:
n1
- : Number of 'A' allelesn2
- : Number of 'B' allelesn12
- : Number of 'AB' individuals Note: Total number of individuals (assuming they are diploid) is N = (n1 + n2) / 2- Returns:
- pValue using exact test
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