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 Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=hsrecombi to link to this page.
RetroSearch is an open source project built by @garambo | Open a GitHub Issue
Search and Browse the WWW like it's 1997 | Search results from DuckDuckGo
HTML:
3.2
| Encoding:
UTF-8
| Version:
0.7.4