Package: paramlink2 1.0.6
Magnus Dehli Vigeland
paramlink2: Parametric Linkage Analysis
Parametric linkage analysis of monogenic traits in medical pedigrees. Features include singlepoint analysis, multipoint analysis via 'MERLIN' (Abecasis et al. (2002) <doi:10.1038/ng786>), visualisation of log of the odds (LOD) scores and summaries of linkage peaks. Disease models may be specified to accommodate phenocopies, reduced penetrance and liability classes. 'paramlink2' is part of the 'pedsuite' package ecosystem, presented in 'Pedigree Analysis in R' (Vigeland, 2021, ISBN:9780128244302).
Authors:
paramlink2_1.0.6.tar.gz
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paramlink2.pdf |paramlink2.html✨
paramlink2/json (API)
NEWS
| # Install 'paramlink2' in R: |
| install.packages('paramlink2', repos = c('https://magnusdv.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/magnusdv/paramlink2/issues
- dominant1 - Dominant linkage analysis example
Last updated 6 months agofrom:243d57dc08. Checks:8 OK. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 04 2025 |
| R-4.5-win | OK | Feb 04 2025 |
| R-4.5-mac | OK | Feb 04 2025 |
| R-4.5-linux | OK | Feb 04 2025 |
| R-4.4-win | OK | Feb 04 2025 |
| R-4.4-mac | OK | Feb 04 2025 |
| R-4.3-win | OK | Feb 04 2025 |
| R-4.3-mac | OK | Feb 04 2025 |
Exports:diseaseModellodlodPeaksmerlinLodpeakSummary
Dependencies:evaluatehighrkinship2knitrlatticeMatrixpedmutpedprobrpedtoolsquadprogxfunyaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Disease models for linkage analysis | diseaseModel |
| Dominant linkage analysis example | dominant1 |
| S3 methods for class 'linkres'. | linkres plot.linkres points.linkres print.linkres summary.linkres |
| Singlepoint LOD score | lod |
| LOD score peaks | lodPeaks peakSummary |
| Multipoint LOD scores by MERLIN | merlinLod |