# Estimation of Recombination Rate and Maternal LD in Half-Sibs

## Documentation for package ‘hsrecombi’ version 0.5.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

bestmapfun | Best fitting genetic-map function
checkCandidates | Candidates for misplacement
countNumbers | Count genotype combinations at 2 SNPs
daughterSire | targetregion: allocation of paternal half-sib families
editraw | Editing results of hsrecombi
felsenstein | Felsenstein's genetic map function
geneticPosition | Estimation of genetic position
genotype.chr | targetregion: progeny genotypes
haldane | Haldane's genetic map function
hapSire | targetregion: sire haplotypes
hsrecombi | Estimation of recombination rate and maternal LD
karlin | Liberman and Karlin's genetic map function
kosambi | Kosambi's genetic map function
LDHScpp | Expectation Maximisation (EM) algorithm
loglikfun | Calculate log-likelihood function
makehap | Make list of imputed sire haplotypes
makehaplist | Make list of sire haplotypes
makehappm | Make list of imputed haplotypes and recombination rate
map.chr | targetregion: physical map
rao | System of genetic-map functions
rao inverse | Approximation to inverse of Rao's system of map functions
rao.inv | Approximation to inverse of Rao's system of map functions
startvalue | Start value for maternal allele and haplotype frequencies
targetregion | Description of the targetregion data set