Other packages > Find by keyword >

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]
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. Accessed 11 Apr. 2025.
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
View hsrecombi citation profile
Other R packages that hsrecombi depends, imports, suggests or enhances
Complete documentation for hsrecombi
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
Downloads during the last 30 days
03/1203/1303/1403/1503/1603/1703/1803/1903/2003/2103/2203/2303/2403/2503/2603/2703/2803/2903/3003/3104/0104/0204/0304/0404/0504/0604/0704/0804/0904/10Downloads for hsrecombi05101520253035TrendBars

Today's Hot Picks in Authors and Packages

extrafrail  
Estimation and Additional Tools for Alternative Shared Frailty Models
Provide estimation and data generation tools for some new multivariate frailty models. This version ...
Download / Learn more Package Citations See dependency  
Rwtss  
Client for Web Time-Series Service
Allows remote access to satellite image time series provided by the web time series service (WTSS) ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
multIntTestFunc  
Provides Test Functions for Multivariate Integration
Provides implementations of functions that can be used to test multivariate integration routines. T ...
Download / Learn more Package Citations See dependency  
GenAlgo  
Classes and Methods to Use Genetic Algorithms for Feature Selection
Defines classes and methods that can be used to implement genetic algorithms for feature selection. ...
Download / Learn more Package Citations See dependency  

24,012

R Packages

207,311

Dependencies

64,867

Author Associations

24,013

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA