hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs

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. 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. For parameter estimation, at least one sire has to be double heterozygous at the investigated pairs of SNPs. Based on recombination rates, genetic distances between markers can be estimated. Markers with unusually large recombination rate to markers in close proximity (i.e. putatively misplaced markers) shall be discarded in this derivation. A workflow description is attached as vignette. *A pipeline is available at GitHub* <https://github.com/wittenburg/hsrecombi> 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: 1.0.1
Depends: R (≥ 3.5.0)
Imports: Rcpp (≥ 1.0.3), hsphase, dplyr, data.table, rlist, quadprog, curl, Matrix
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, formatR, AlphaSimR (≥ 0.13.0), doParallel, ggplot2
Published: 2023-06-07
DOI: 10.32614/CRAN.package.hsrecombi
Author: Dörte Wittenburg [aut, cre]
Maintainer: Dörte Wittenburg <wittenburg at fbn-dummerstorf.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Language: en-GB
Materials: NEWS
CRAN checks: hsrecombi results


Reference manual: hsrecombi.pdf
Vignettes: Description of the workflow for constructing a genetic map using *hsrecombi*


Package source: hsrecombi_1.0.1.tar.gz
Windows binaries: r-devel: hsrecombi_1.0.1.zip, r-release: hsrecombi_1.0.1.zip, r-oldrel: hsrecombi_1.0.1.zip
macOS binaries: r-release (arm64): hsrecombi_1.0.1.tgz, r-oldrel (arm64): hsrecombi_1.0.1.tgz, r-release (x86_64): hsrecombi_1.0.1.tgz, r-oldrel (x86_64): hsrecombi_1.0.1.tgz
Old sources: hsrecombi archive


Please use the canonical form https://CRAN.R-project.org/package=hsrecombi to link to this page.