R: LD statistics for two multiallelic markers

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 LD22

    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 <- system.file("tests/2ld/kbyl.dat")
    h <- scan(filespec,skip=1)
    t <- LDkl(9,5,h,213*2,verbose=TRUE)

    ## End(Not run)

[Package gap version 1.2.1 Index]