kbyl {gap}R Documentation

LD statistics for two multiallelic loci

Description

LD statistics for two multiallelic loci

Usage

kbyl(n1,n2,h,n,optrho=2)

Arguments

n1 number of alleles at marker 1
n2 number of alleles at marker 2
h a vector of haplotype frequencies
n number of haplotypes
optrho type of contingency table association, 0=Pearson, 1=Tschuprow, 2=Cramer (default)

Value

The returned value is a list containing:

n1 the number of alleles at marker 1
n2 the number of alleles at marker 2
h the haplotype frequency vector
n the number of haplotypes
VarDp variance of D'
Dijtable table of Dij
Dmaxtable table of Dmax
Dijptable table of Dij'
VarDijtable table of variances for Dij
VarDijptable table of variances for Dij'
x2 the Chi-squared statistic
seX2 the variance of x2
rho the measure of association
seR the standard error of rho
optrho the method for calculating rho
klinfo the Kullback-Leibler information

References

Bishop YMM, Fienberg SE, Holland PW (1975) Discrete Multivariate Analysis – Theory and Practice, The MIT press

Cramer H (1946) Mathematical Methods of Statistics. Princeton Univ. Press

Zapata C, Carollo C, Rodriquez S (2001) Sampleing variance and distribution of the D' measure of overall gametic disequilibrium between multiallelic loci. Ann. Hum. Genet. 65: 395-406

Zhao, JH (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics 20:1325-1326

Note

adapted from 2ld.c

Author(s)

Jing hua Zhao

See Also

tbyt

Examples

## Not run: 
# example of two SNPs
h <- c(0.442356,0.291532,0.245794,0.020319)
n <- 481*2
kbyl(2,2,h,n)
## End(Not run)

[Package gap version 1.0-2 Index]