gap (version 1.1-16)

klem: Haplotype frequency estimation based on a genotype table of two multiallelic markers

Description

Haplotype frequency estimation using expectation-maximization algorithm based on a table of genotypes of two multiallelic markers.

Usage

klem(obs, k=2, l=2)

Arguments

obs

a table of genotype counts

k

number of alleles at marker 1

l

number of alleles at marker 2

Value

The returned value is a list containing:

h

haplotype Frequencies

l0

log-likelihood under linkage equilibrium

l1

log-likelihood under linkage disequilibrium

Details

The dimension of the genotype table should be k*(k+1)/2 x l*(l+1)/2.

Modified from 2ld.c.

See Also

genecounting

Examples

## 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)