hsrecombi
Estimation of Recombination Rate and Maternal LD in Half-Sibs
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* <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>.
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CRAN Check Status
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| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | OK |
| r-devel-macos-arm64 | OK |
| r-devel-windows-x86_64 | OK |
| r-oldrel-macos-arm64 | OK |
| r-oldrel-macos-x86_64 | OK |
| r-oldrel-windows-x86_64 | OK |
| r-patched-linux-x86_64 | OK |
| r-release-linux-x86_64 | OK |
| r-release-macos-arm64 | OK |
| r-release-macos-x86_64 | OK |
| r-release-windows-x86_64 | OK |
Check History
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 3, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Apr 2, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'hsrecombi_workflow.Rmd' using rmarkdown Quitting from hsrecombi_workflow.Rmd:136-166 [recombination-rate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rla ...[truncated]... md' failed with diagnostics: task 2 failed - "argument is of length zero" --- failed re-building 'hsrecombi_workflow.Rmd' SUMMARY: processing the following file failed: 'hsrecombi_workflow.Rmd' Error: Vignette re-building failed. Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 31, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 27, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building ‘hsrecombi_workflow.Rmd’ using rmarkdown Quitting from hsrecombi_workflow.Rmd:136-166 [recombination-rate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <error/rla ...[truncated]... md' failed with diagnostics: task 2 failed - "argument is of length zero" --- failed re-building ‘hsrecombi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘hsrecombi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 24, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 14, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘hsrecombi_workflow.Rmd’ using rmarkdown Quitting from hsrecombi_workflow.Rmd:136-166 [recombination-rate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <err ...[truncated]... md' failed with diagnostics: task 1 failed - "argument is of length zero" --- failed re-building ‘hsrecombi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘hsrecombi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 13, 2026
ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 10, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: ... --- re-building ‘hsrecombi_workflow.Rmd’ using rmarkdown Quitting from hsrecombi_workflow.Rmd:136-166 [recombination-rate] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ <err ...[truncated]... md' failed with diagnostics: task 1 failed - "argument is of length zero" --- failed re-building ‘hsrecombi_workflow.Rmd’ SUMMARY: processing the following file failed: ‘hsrecombi_workflow.Rmd’ Error: Vignette re-building failed. Execution halted