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| countNumbers | Count genotype combinations at 2 SNPs |
| daughterSire | targetregion: allocation of paternal half-sib families |
| editraw | editraw |
| genotype.chr | targetregion: progeny genotypes |
| hapSire | targetregion: sire haplotypes |
| hsrecombi | hsrecombi |
| LDHScpp | Expectation Maximisation (EM) algorithm |
| loglikfun | Calculate log-likelihood function |
| makehap | makehap |
| makehaplist | makehaplist |
| map.chr | targetregion: physical map |
| startvalue | startvalue |
| targetregion | Description of the targetregion data set |