GOLD  Available Statistics
Notation
Consider markers A and B, with r and c alleles,
respectively. As usual, define the following variables based
on observed haplotype counts:
These can be used to derive the haplotype frequencies:
The available measures of disequilibrium are defined in terms
of the above quantities.
Lewontin's Disequilibrium Coefficient D and D'
The definition of Hedrick (1987), which allows for multiallelic
markers is used:
DeltaSquared Measure of disequilibrium
This is only defined for biallelic markers. The conventional
definition (see for example, Devlin and Risch, 1995) is used:
Other Measures of Association  ChiSquared
The usual contingency table chisquared is calculated, and
its significant is estimated from an asymptotic distribution
with (r1)(c1) degrees of freedom.
Other Measures of Association  Uncertainty Coefficient
U
The definition of Press, Teukolsky, Vetterling and Flannery,
NRC (2nd Edition), is used:
H(A), H(B), H(A,B) refer to the informativeness of marker
A, marker B, and the two marker genotypes together. U refers
to how much information one marker provides on the other's genotype.
It varies between 0 (independent) and 1 (completely dependent).
Other Measures of Association  Cramer's V
This is a transformation of the chisquared statistic into
the zero to one interval and is useful for comparing the relative
intensity of association between marker pairs with the r
and c. The definition of Press, Teukolsky, Vetterling
and Flannery, NRC (2nd Edition), is used:
