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hsrecombi  

Estimation of Recombination Rate and Maternal LD in Half-Sibs
View on CRAN: Click here


Download and install hsrecombi package within the R console
Install from CRAN:
install.packages("hsrecombi")

Install from Github:
library("remotes")
install_github("cran/hsrecombi")

Install by package version:
library("remotes")
install_version("hsrecombi", "1.0.1")



Attach the package and use:
library("hsrecombi")
Maintained by
Dörte Wittenburg
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-03-04
Latest Update: 2023-06-07
Description:
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* Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" . Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" .
How to cite:
Dörte Wittenburg (2020). hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs. R package version 1.0.1, https://cran.r-project.org/web/packages/hsrecombi
Previous versions and publish date:
0.1.3 (2020-03-04 11:20), 0.3.0 (2020-05-28 11:00), 0.3.1 (2020-08-27 13:10), 0.3.2 (2020-10-14 10:40), 0.3.4 (2021-03-23 09:30), 0.4.1 (2022-03-24 09:40), 0.4.2 (2022-03-27 16:30), 0.5.0 (2022-11-29 14:10), 0.5.1 (2022-12-01 13:20)
Other packages that cited hsrecombi R package
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Other R packages that hsrecombi depends, imports, suggests or enhances
Functions, R codes and Examples using the hsrecombi R package
Some associated functions: LDHScpp . bestmapfun . checkCandidates . countNumbers . daughterSire . editraw . felsenstein . geneticPosition . genotype.chr . haldane . hapSire . hsrecombi . karlin . kosambi . loglikfun . makehap . makehaplist . makehappm . map.chr . rao-inverse . rao . startvalue . targetregion . 
Some associated R codes: RcppExports.R . daughterSire.R . functions.R . genotype.chr.R . hapSire.R . hsrecombi.R . map.chr.R . targetregion.R .  Full hsrecombi package functions and examples
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