Description Usage Arguments Value References Examples

List of sire haplotypes is set up in the format required for
hsrecombi. Sire haplotypes are imputed from progeny genotypes using R
package `hsphase`

. Furthermore, recombination rate estimates between
adjacent SNPs from hsphase are reported.

1 | ```
makehappm(sireID, daughterSire, genotype.chr, nmin = 30)
``` |

`sireID` |
vector (LEN N) of IDs of all sires |

`daughterSire` |
vector (LEN n) of sire ID for each progeny |

`genotype.chr` |
matrix (DIM n x p) of progeny genotypes on a single chromosome with p SNPs |

`nmin` |
scalar, minimum number of progeny required, default 1 |

hap list (LEN 2) of lists. For each sire:

`famID`

list (LEN N) of vectors (LEN n.progeny) of progeny indices relating to lines in genotype matrix

`sireHap`

list (LEN N) of matrices (DIM 2 x p) of sire haplotypes (0, 1) on investigated chromosome

- probRec
vector (LEN p - 1) of proportion of recombinant progeny over all families between adjacent SNPs

- numberRec
list (LEN N) of vectors (LEN n.progeny) of number of recombination events per animal

Ferdosi, M., Kinghorn, B., van der Werf, J., Lee, S. & Gondro, C. (2014) hsphase: an R package for pedigree reconstruction, detection of recombination events, phasing and imputation of half-sib family groups BMC Bioinformatics 15:172. https://CRAN.R-project.org/package=hsphase

1 2 | ```
data(targetregion)
hap <- makehappm(unique(daughterSire), daughterSire, genotype.chr)
``` |

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