Haplotype frequency estimation based on a genotype table of two multiallelic markers
Haplotype frequency estimation using expectation-maximization algorithm based on a table of genotypes of two multiallelic markers.
klem(obs, k=2, l=2)
obs |
a table of genotype counts |
k |
number of alleles at marker 1 |
l |
number of alleles at marker 2 |
The dimension of the genotype table should be k*(k+1)/2 x l*(l+1)/2.
Modified from 2ld.c.
The returned value is a list containing:
h |
haplotype Frequencies |
l0 |
log-likelihood under linkage equilibrium |
l1 |
log-likelihood under linkage disequilibrium |
Jing Hua Zhao
## Not run:
# an example with known genotype counts
z <- klem(obs=1:9)
# an example with imputed genotypes at SH2B1
cwd <- getwd()
cs.dir <- file.path(path.package("gap"),"tests/klem")
setwd(cs.dir)
dir()
source("SH2B1.R",echo=TRUE)
setwd(cwd)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.