gap: LDkl – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

gap

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

Note

adapted from 2ld.c

Author(s)

Jing Hua Zhao

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)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21