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 can be discarded in this derivation. *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" .


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0.3.4 by Dörte Wittenburg, 10 months ago

Browse source code at

Authors: Dörte Wittenburg [aut, cre]

Documentation:   PDF Manual  

GPL (>= 2) license

Imports Rcpp, hsphase, dplyr, data.table, rlist, quadprog, curl

Suggests knitr, rmarkdown, formatR, AlphaSimR, doParallel, ggplot2

Linking to Rcpp

See at CRAN