| 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. MIT Press, Cambridge, Mass. ISBN 9780262021135.
Cramer H (1946). Mathematical Methods of Statistics. Princeton Univ. Press.
Zapata C, Carollo C, Rodriguez S (2001). “Sampling variance and distribution of the D' measure of overall gametic disequilibrium between multiallelic loci.” Ann Hum Genet, 65(Pt 4), 395-406. ISSN 0003-4800 (Print) 0003-4800, doi:10.1017/s0003480001008697.
Zhao JH (2004). “2LD. GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.” Bioinformatics, 20(8), 1325-6. ISSN 1367-4803 (Print) 1367-4803, doi:10.1093/bioinformatics/bth071.
See Also
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"
# The data is now available from 2ld in Haplotype-Analysis
filespec <- system.file("kbyl.dat")
h <- scan(filespec,skip=1)
t <- LDkl(9,5,h,213*2,verbose=TRUE)
## End(Not run)