gap (version 1.1-1)

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

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