gap (version 1.1-1)

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

# 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)