Package org.snpsift
Class VcfLd
- java.lang.Object
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- org.snpsift.VcfLd
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public class VcfLd extends java.lang.Object
Calculate Linkage Disequilibrium Reference: "Principles of population genetics (4th edition)" Hartl & Clark, pages 73 to 81 Note: I try to follow the same notation as the book. WARNING: I assume that the organism is diploid (i.e. it has two chromosomes)- 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 VcfLd()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description double
getD()
double
getDmax()
double
getDmin()
double
getDprime()
double
getpA()
double
getpB()
double
getQa()
double
getQb()
double
getrSquare()
double
ld()
Calculate linkage disequilibrium parametersdouble
ld(org.snpeff.vcf.VcfEntry vcfEntryA, org.snpeff.vcf.VcfEntry vcfEntryB)
Calculate linkage disequilibrium parameterjava.lang.String
sanityCheck(org.snpeff.vcf.VcfEntry vcfEntryA, org.snpeff.vcf.VcfEntry vcfEntryB)
Return an error message if any problem is found or empty string if it is OK.void
setCount(int countAB, int countAb, int countaB, int countab, int countA, int counta, int countB, int countb)
Set counters in order to calculate LD parameters
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Method Detail
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getD
public double getD()
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getDmax
public double getDmax()
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getDmin
public double getDmin()
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getDprime
public double getDprime()
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getpA
public double getpA()
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getpB
public double getpB()
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getQa
public double getQa()
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getQb
public double getQb()
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getrSquare
public double getrSquare()
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ld
public double ld()
Calculate linkage disequilibrium parameters- Returns:
- linkage disequilibrium between 'A' and 'B'
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ld
public double ld(org.snpeff.vcf.VcfEntry vcfEntryA, org.snpeff.vcf.VcfEntry vcfEntryB)
Calculate linkage disequilibrium parameter- Parameters:
vcfEntryA
- : Vcf entry at locus 'A'vcfEntryB
- : Vcf entry at locus 'B'- Returns:
- linkage disequilibrium between 'A' and 'B'
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sanityCheck
public java.lang.String sanityCheck(org.snpeff.vcf.VcfEntry vcfEntryA, org.snpeff.vcf.VcfEntry vcfEntryB)
Return an error message if any problem is found or empty string if it is OK.- Returns:
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setCount
public void setCount(int countAB, int countAb, int countaB, int countab, int countA, int counta, int countB, int countb)
Set counters in order to calculate LD parameters- Parameters:
countAB
-countAb
-countaB
-countab
-countA
-counta
-countB
-countb
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