kbyl {gap} | R Documentation |
LD statistics for two multiallelic loci
kbyl(n1,n2,h,n,optrho=2)
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) |
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 |
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
adapted from 2ld.c
Jing hua Zhao
## Not run: # example of two SNPs h <- c(0.442356,0.291532,0.245794,0.020319) n <- 481*2 kbyl(2,2,h,n) ## End(Not run)