Description Usage Arguments Details Value Author(s) References Examples
Functions for computing LD measures for predefined (or estimated) allele frequency values and a predefined (or estimated) disequilibrium coefficient value.
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pA1 |
Allele frequency for the first SNP |
pA2 |
Allele frequency for the second SNP |
D |
Disequilibrium coefficient |
The LD measures available in GUSLD are:
Dcoef
The disequilibrium coefficient \insertCitelewontin1960evolutionGUSLD defined as D=p_{A_1A_2}-p_{A_1}p_{A_2}
Dprime
The normalized disequilibrium coefficient \insertCitelewontin1964geneticsGUSLD defined as D'=D/D_{max} where D_{max} = min(p_{A_1}p_{A_2},(1-p_{A_1})(1-p_{A_2})) if D>0 and D_{max} = min(p_{A_1}(1-p_{A_2}),(1-p_{A_1})p_{A_2})
r2
The squared correlation coefficient \insertCitehill1968TAGGUSLD defined as r^2=D^2/√{p_{A_1}p_{A_2}(1-p_{A_1})(1-p_{A_2})}
where p_{A_1A_2} is the probability of observing a haplotype containing the reference allele at both loci, p_{A_1} is the major allele frequency at the first SNP and p_{A_2} is the allele frequency at the second SNP. One can also specify their own LD measure (see examples below).
A numeric value giving the value of the LD measure
Timothy P. Bilton
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