Estimation of Recombination Rate and Maternal LD in Half-Sibs

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Documentation for package ‘hsrecombi’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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 estimate 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