Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least one sire has to be double heterozygous at the investigated pairs of SNPs. The implementation relies on paternal half-sib families. If maternal half- sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" <doi:10.3389/fgene.2018.00186>. Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" <doi:10.1534/genetics.111.137521>.
| Version: | 0.3.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | Rcpp (≥ 1.0.3), hsphase, dplyr, data.table, rlist, quadprog |
| LinkingTo: | Rcpp |
| Published: | 2020-05-28 |
| Author: | Dörte Wittenburg [aut, cre] |
| Maintainer: | Dörte Wittenburg <wittenburg at fbn-dummerstorf.de> |
| License: | GPL-2 | GPL-3 [expanded from: GPL (≥ 2)] |
| NeedsCompilation: | yes |
| Materials: | NEWS |
| CRAN checks: | hsrecombi results |
| Reference manual: | hsrecombi.pdf |
| Package source: | hsrecombi_0.3.0.tar.gz |
| Windows binaries: | r-devel: hsrecombi_0.3.0.zip, r-release: hsrecombi_0.3.0.zip, r-oldrel: hsrecombi_0.3.0.zip |
| macOS binaries: | r-release: hsrecombi_0.3.0.tgz, r-oldrel: hsrecombi_0.3.0.tgz |
| Old sources: | hsrecombi archive |
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