Estimate allele frequencies and test for Hardy-Weinberg equilibrium with a tri-allelic ABO system.
Function HWABO takes four genotype counts ("A","B","AB","OO") and
estimates the three allele frequencies using the EM algorithm.
HWABO(x, p = c(1/3, 1/3, 1/3), maxiter = 50, tol = 1e-10, verbose = TRUE)
x |
a vector with genotype counts ("A","B","AB","OO"). |
p |
a vector with initial allele frequencies (by default (1/3,1/3,1/3)). |
maxiter |
maximum number of iterations. |
tol |
tolerance for convergence, 1e-10 by default |
verbose |
print iteration history or not. |
pn |
vector with estimated allele frequencies. |
It.hist |
iteration history with log-likelihood. |
expected |
expected genotype counts under HWE. |
Jan Graffelman jan.graffelman@upc.edu
x <- c(fA=182,fB=60,nAB=17,nOO=176) al.fre <- HWABO(x) #al2 <- HWABO(x,p=c(0.99,0.01,0.01),maxiter=25) #al3 <- HWABO(x,p=c(0.01,0.99,0.01),maxiter=25) #al4 <- HWABO(x,p=c(0.01,0.01,0.99),maxiter=25)
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