LDkl {gap}R Documentation

LD statistics for two multiallelic markers

Description

LD statistics for two multiallelic loci. For two diallelic makers, the familiar r^2 has standard error seX2.

Usage

LDkl(n1=2,n2=2,h,n,optrho=2,verbose=FALSE)

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)
verbose detailed output of individual statistics

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
Dp D'
VarDp variance of D'
Dijtable table of Dij
VarDijtable table of variances for Dij
Dmaxtable table of Dmax
Dijptable table of Dij'
VarDijptable table of variances for Dij'
X2table table of Chi-squares (based on Dij)
ptable table of p values
x2 the Chi-squared statistic
seX2 the standard error of x2/n
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

LD22

Examples

## Not run: 
# two examples in the C program 2LD:
# two SNPs as in 2by2.dat
# this can be compared with output from tbyt

h <- c(0.442356,0.291532,0.245794,0.020319)
n <- 481*2
t <- LDkl(2,2,h,n)
t

# two multiallelic markers as in kbyl.dat
# the two-locus haplotype vector is in file "kbyl.dat"

filespec <- file.path(.path.package("gap"),"tests/kbyl.dat")
h <- scan(filespec,skip=1)
t <- LDkl(9,5,h,213*2,verbose=TRUE)
## End(Not run)

[Package gap version 1.0-17 Index]