RZooRoH
Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes
Description
Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) <doi:10.1111/mec.14324> and Druet and Gautier (2022) <doi:10.1016/j.tpb.2022.03.001>.
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CRAN Check Status
Show all 14 flavors
| 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 | ERROR |
| 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 details (1 non-OK)
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'zooroh-vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `62aeb0f6c4f979fe3124502809c501c0dad7e77d.pdf' not found: using draft setting. Error: processing vignette 'zooroh-vignette.Rmd' failed with diagnostics: LaTeX failed to compile D:/RCompile/CRANpkg/local/4.4/RZooRoH.Rcheck/vign_test/RZooRoH/vignettes/zooroh-vignette.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See zooroh-vignette.log for more info. --- failed re-building 'zooroh-vignette.Rmd' SUMMARY: processing the following file failed: 'zooroh-vignette.Rmd' Error: Vignette re-building failed. Execution halted
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ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 30, 2026
re-building of vignette outputs
Error(s) in re-building vignettes: --- re-building 'zooroh-vignette.Rmd' using rmarkdown ! Package pdftex.def Error: File `62aeb0f6c4f979fe3124502809c501c0dad7e77d.pdf' not found: using draft setting. Error: processing vignette 'zooroh-vignette.Rmd ...[truncated]... tinytex/r/#debugging for debugging tips. See zooroh-vignette.log for more info. --- failed re-building 'zooroh-vignette.Rmd' SUMMARY: processing the following file failed: 'zooroh-vignette.Rmd' Error: Vignette re-building failed. Execution halted