Package: ibdfindr 0.5.0
Magnus Dehli Vigeland
ibdfindr: HMM Toolkit for Inferring IBD Segments from SNP Data
Implements continuous-time hidden Markov models (HMMs) to infer identity-by-descent (IBD) segments shared by two individuals. Supports two- and three-state models using single-nucleotide polymorphism (SNP) genotypes or genotype likelihoods. Provides posterior probabilities at each marker (forward-backward algorithm), prediction of IBD segments (Viterbi algorithm), and functions for visualising results. Supports both autosomal data and X-chromosomal data. The methodology and package are described in Vigeland et al. (2026) <doi:10.1016/j.fsigen.2025.103409>.
Authors:
ibdfindr_0.5.0.tar.gz
ibdfindr_0.5.0.zip(r-4.7-any)ibdfindr_0.5.0.zip(r-4.6-any)ibdfindr_0.5.0.zip(r-4.5-any)
ibdfindr_0.5.0.tgz(r-4.6-any)ibdfindr_0.5.0.tgz(r-4.5-any)
ibdfindr_0.5.0.tar.gz(r-4.7-any)ibdfindr_0.5.0.tar.gz(r-4.6-any)
ibdfindr_0.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ibdfindr/json (API)
| # Install 'ibdfindr' in R: |
| install.packages('ibdfindr', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/ibdfindr/issues
- brothersX - Dataset with X-chromosomal SNP genotypes for two brothers
- cousinsDemo - Dataset with autosomal SNP genotypes for two cousins
- sibsGL - Dataset with genotype likelihoods for two full siblings
Last updated from:4fe06909e7. Checks:7 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 202 | ||
| source / vignettes | OK | 279 | ||
| linux-release | OK | 182 | ||
| windows-devel | OK | 122 | ||
| windows-release | OK | 89 | ||
| windows-oldrel | OK | 135 | ||
| wasm-release | OK | 101 |
Exports:computePRestimateDropoutfindIBDfindSegmentsfitHMMibdPosteriorsplotIBDproblemMarkersreadGLtotalLoglik
Dependencies:clicpp11evaluatefarverforrelggplot2gluegtablehighribdsim2isobandkinship2knitrlabelinglatticelifecyclelpSolveMatrixmirainanonextpedmutpedprobrpedtoolsquadprogR6RColorBrewerRcppribdrlangS7scalesslamvctrsverbalisrviridisLitewithrxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Dataset with X-chromosomal SNP genotypes for two brothers | brothersX |
| Precision and Recall for IBD segment calls | computePR |
| Dataset with autosomal SNP genotypes for two cousins | cousinsDemo |
| Estimate allelic dropout | estimateDropout |
| All-in-one workflow for finding IBD segments | findIBD |
| Identify IBD segments | findSegments |
| Fit a Hidden Markov Model to genotype data | fitHMM |
| IBD posteriors | ibdPosteriors |
| Plot IBD segments and posteriors | plotIBD |
| Identify problematic markers | problemMarkers |
| Read genotype likelihood data | readGL |
| Dataset with genotype likelihoods for two full siblings | sibsGL |
| Total log-likelihood for observed data | totalLoglik |