| LD22 {gap} | R Documentation |
LD statistics for two SNPs.
LD22(h, n)
h |
a vector of haplotype frequencies. |
n |
number of haplotypes. |
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.
The returned value is a list containing:
the original haplotype frequency vector
the number of haplotypes
the linkage disequilibrium parameter
the variance of D
the maximum of D
the variance of Dmax
the scaled disequilibrium parameter
the variance of Dprime
the Chi-squared statistic
the log(OR) statistic
the var[log(OR)] statistic
extracted from 2ld.c.
Jing Hua Zhao
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
## Not run: h <- c(0.442356,0.291532,0.245794,0.020319) n <- 481*2 t <- LD22(h,n) ## End(Not run)