LD22: LD statistics for two diallelic markers

Description

LD statistics for two SNPs.

It is possible to perform permutation test of $r^2$ by re-ordering the genotype through R's sample function, obtaining the haplotype frequencies by gc.em or genecounting, supplying the estimated haplotype frequencies to the current function and record x2, and comparing the observed x2 and that from the replicates.

Usage

LD22(h,n)

Arguments

a vector of haplotype frequencies

number of haplotypes

Value

h: the original haplotype frequency vector
n: the number of haplotypes
D: the linkage disequilibrium parameter
VarD: the variance of D
Dmax: the maximum of D
VarDmax: the variance of Dmax
Dprime: the scaled disequilibrium parameter
VarDprime: the variance of Dprime
x2: the Chi-squared statistic
lor: the log(OR) statistic
vlor: the var[log(OR)] statistic

References

Zabetian CP, Buxbaum SG, Elston RC, Kohnke MD, Anderson GM, Gelernter J, Cubells JF. The structure of linkage disequilibrium at the DBH locus strongly influences the magnitude of association between diallelic markers and plasma dopamine beta-hydroxylase activity Am J Hum Genet 72: 1389-1400 Zapata C, Alvarez G, Carollo C (1997) Approximate variance of the standardized measure of gametic disequilibrium D'. Am. J. Hum. Genet. 61:771-774

Examples

Run this code

## Not run: 
# h <- c(0.442356,0.291532,0.245794,0.020319)
# n <- 481*2
# t <- LD22(h,n)
# t
# ## End(Not run)