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. 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" <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>.

Version: 0.3.2
Depends: R (≥ 3.5.0)
Imports: Rcpp (≥ 1.0.3), hsphase, dplyr, data.table, rlist, quadprog
LinkingTo: Rcpp
Suggests: knitr, rmarkdown, formatR, AlphaSimR (≥ 0.13.0), doParallel, ggplot2
Published: 2020-10-14
Author: Dörte Wittenburg [aut, cre]
Maintainer: Dörte Wittenburg <wittenburg at fbn-dummerstorf.de>
License: GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
NeedsCompilation: yes
Materials: NEWS
CRAN checks: hsrecombi results


Reference manual: hsrecombi.pdf
Vignettes: Workflow description with hsrecombi
Package source: hsrecombi_0.3.2.tar.gz
Windows binaries: r-devel: hsrecombi_0.3.2.zip, r-release: hsrecombi_0.3.2.zip, r-oldrel: hsrecombi_0.3.2.zip
macOS binaries: r-release: hsrecombi_0.3.2.tgz, r-oldrel: hsrecombi_0.3.2.tgz
Old sources: hsrecombi archive


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