Package: hsrecombi 1.0.1

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>.

Authors:Dörte Wittenburg [aut, cre]

hsrecombi_1.0.1.tar.gz
hsrecombi_1.0.1.zip(r-4.5)hsrecombi_1.0.1.zip(r-4.4)hsrecombi_1.0.1.zip(r-4.3)
hsrecombi_1.0.1.tgz(r-4.4-x86_64)hsrecombi_1.0.1.tgz(r-4.4-arm64)hsrecombi_1.0.1.tgz(r-4.3-x86_64)hsrecombi_1.0.1.tgz(r-4.3-arm64)
hsrecombi_1.0.1.tar.gz(r-4.5-noble)hsrecombi_1.0.1.tar.gz(r-4.4-noble)
hsrecombi_1.0.1.tgz(r-4.4-emscripten)hsrecombi_1.0.1.tgz(r-4.3-emscripten)
hsrecombi.pdf |hsrecombi.html✨
hsrecombi/json (API)
NEWS

# Install 'hsrecombi' in R:
install.packages('hsrecombi', repos = c('https://wittenburg.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • daughterSire - Targetregion: allocation of paternal half-sib families
  • genotype.chr - Targetregion: progeny genotypes
  • hapSire - Targetregion: sire haplotypes
  • map.chr - Targetregion: physical map

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 7 scripts 369 downloads 16 exports 30 dependencies

Last updated 1 years agofrom:965415266c. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 07 2024
R-4.5-win-x86_64OKNov 07 2024
R-4.5-linux-x86_64OKNov 07 2024
R-4.4-win-x86_64OKNov 07 2024
R-4.4-mac-x86_64OKNov 07 2024
R-4.4-mac-aarch64OKNov 07 2024
R-4.3-win-x86_64OKNov 07 2024
R-4.3-mac-x86_64OKNov 07 2024
R-4.3-mac-aarch64OKNov 07 2024

Exports:bestmapfuncheckCandidateseditrawfelsensteingeneticPositionhaldanehsrecombikarlinkosambiLDHScppmakehapmakehaplistmakehappmraorao.invstartvalue

Dependencies:clicurldata.tabledplyrfansigenericsgluehsphasejsonlitelatticelifecyclemagrittrMatrixpillarpkgconfigquadprogR6RcppRcppArmadillorlangrlistsnowsnowfalltibbletidyselectutf8vctrswithrXMLyaml

Description of the workflow for constructing a genetic map using hsrecombi

D. Wittenburg

Rendered fromhsrecombi_workflow.Rmdusingknitr::rmarkdownon Nov 07 2024.

Last update: 2023-06-07
Started: 2020-08-27