gap (version 1.2.3-1)

LDkl: 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

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)
# }