gap (version 1.1-20)

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

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

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

See Also

LDkl

Examples

# NOT RUN {
h <- c(0.442356,0.291532,0.245794,0.020319)
n <- 481*2
t <- LD22(h,n)
t
# }