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.

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.

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

Modified from 2ld.c.

Value

The returned value is a list containing:

• h haplotype Frequencies.

• l0 log-likelihood under linkage equilibrium.

• l1 log-likelihood under linkage disequilibrium.

See also

genecounting

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
# an example with known genotype counts 
z <- klem(obs=1:9)
# an example with imputed genotypes at SH2B1
source(file.path(find.package("gap"),"scripts","SH2B1.R"),echo=TRUE)
} # }