gap (version 0.4)

kbyl: LD statistics for two multiallelic loci

Description

LD statistics for two multiallelic loci

Usage

kbyl(n1,n2,h,n,optrho)

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)

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
• VarDp
  variance of D'
• Dijtable
  table of Dij
• Dmaxtable
  table of Dmax
• Dijptable
  table of Dij'
• VarDijtable
  table of variances for Dij
• VarDijptable
  table of variances for Dij'
• x2
  the Chi-squared statistic
• seX2
  the variance of x2
• 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

See Also

tbyt

Examples

# example of two SNPs
h <- c(0.442356,0.291532,0.245794,0.020319)
n <- 481*2
kbyl(2,2,h,n)