LD statistics for two diallelic markers

Usage

LD22(h, n)

Arguments

h: a vector of haplotype frequencies.
n: number of haplotypes.

Value

The returned value is a list containing:

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.

Details

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.

Note

extracted from 2ld.c, worked 28/6/03, tables are symmetric do not fix, see kbyl below

References

Zabetian CP, Buxbaum SG, Elston RC, Köhnke MD, Anderson GM, Gelernter J, Cubells JF (2003). “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(6), 1389-400. doi:10.1086/375499 .

Zapata C, Alvarez G, Carollo C (1997). “Approximate variance of the standardized measure of gametic disequilibrium D'.” Am J Hum Genet, 61(3), 771-4. doi:10.1016/s0002-9297(07)64342-0 .

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
h <- c(0.442356,0.291532,0.245794,0.020319)
n <- 481*2
t <- LD22(h,n)
} # }