Use LD R-Squared when you need to compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))). Enter LD coefficient D, Allele A frequency, and Allele B frequency using the definitions and units below so the result can be reproduced.

LD coefficient D

A finite measured or assumed value.

Allele A frequency

A finite measured or assumed value from 0 through 1.

Allele B frequency

A finite measured or assumed value from 0 through 1.

The published tool contract uses this rule: Compute squared linkage disequilibrium r2 = D^2 / (p(A) * (1 - p(A)) * p(B) * (1 - p(B))).

r-squared

The calculated r-squared.

The calculation does not propagate measurement uncertainty, sampling error, or biological and chemical variability. Allele A frequency must remain between 0 and 1; Allele B frequency must remain between 0 and 1.

Retain the original LD coefficient D, Allele A frequency, and Allele B frequency values and their units alongside the result. LD Coefficient D is useful when you instead need to compute linkage disequilibrium coefficient D = f(AB) - p(A) * p(B); the signed result may be negative. Allele Count Total provides another view by helping you count total allele copies at a diploid locus as twice the number of individuals.

• LD Coefficient D

  Compute linkage disequilibrium coefficient D = f(AB) - p(A) * p(B); the signed result may be negative.

• Allele Count Total

  Count total allele copies at a diploid locus as twice the number of individuals.

• Allele Freq From Counts

  Compute allele A frequency p = (2*AA + AB) / (2*(AA + AB + BB)) from genotype counts.