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

### Note

adapted from 2ld.c.

### Author(s)

Jing Hua Zhao

### 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

### 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 1.2.3-6 Index]