hsrecombi

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* https://github.com/wittenburg/hsrecombi 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.

Last 30 days

This package has been downloaded 320 times in the last 30 days. Enough downloads to make a small wave in the niche community. The curiosity is spreading! The following heatmap shows the distribution of downloads per day. Yesterday, it was downloaded 7 times.

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Last 365 days

This package has been downloaded 4,640 times in the last 365 days. Now we’re talking! This work is officially 'heard of in academic circles', just like those wild research papers on synthetic bananas. The day with the most downloads was Sep 11, 2024 with 48 downloads.

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