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. At least one sire has to be double heterozygous at the investigated pairs of SNPs. 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. 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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0.3.2 by Dörte Wittenburg, 3 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

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

Linking to Rcpp

See at CRAN