Package: rres 1.1
rres: Realized Relatedness Estimation and Simulation
Functions for studying realized genetic relatedness between people. Users will be able to simulate inheritance patterns given pedigree structures, generate SNP marker data given inheritance patterns, and estimate realized relatedness between pairs of individuals using SNP marker data. See Wang (2017) <doi:10.1534/genetics.116.197004>. This work was supported by National Institutes of Health grants R37 GM-046255.
Authors:
rres_1.1.tar.gz
rres_1.1.zip(r-4.5)rres_1.1.zip(r-4.4)rres_1.1.zip(r-4.3)
rres_1.1.tgz(r-4.4-x86_64)rres_1.1.tgz(r-4.4-arm64)rres_1.1.tgz(r-4.3-x86_64)rres_1.1.tgz(r-4.3-arm64)
rres_1.1.tar.gz(r-4.5-noble)rres_1.1.tar.gz(r-4.4-noble)
rres_1.1.tgz(r-4.4-emscripten)rres_1.1.tgz(r-4.3-emscripten)
rres.pdf |rres.html✨
rres/json (API)
| # Install 'rres' in R: |
| install.packages('rres', repos = c('https://bowenwang7.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bowenwang7/rres/issues
Last updated 6 years agofrom:1808f80aa1. Checks:OK: 4 NOTE: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 25 2024 |
| R-4.5-win-x86_64 | NOTE | Oct 25 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 25 2024 |
| R-4.4-win-x86_64 | NOTE | Oct 25 2024 |
| R-4.4-mac-x86_64 | NOTE | Oct 25 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 25 2024 |
| R-4.3-win-x86_64 | OK | Oct 25 2024 |
| R-4.3-mac-x86_64 | OK | Oct 25 2024 |
| R-4.3-mac-aarch64 | OK | Oct 25 2024 |
Exports:check.pedinfofgl2ibdfgl2relatednessget.pedindexgrm.matrixgrm.pairibd.lengthibd.markeribd.proportionibd.segmentld.weightspopulate.snpread.plink.binaryread.plink.textrecode.ibdrecode.snpdatasim.haplotypesim.recombwrite.ibdhaplo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Realized Relatedness Rtools | r3-package r3 |
| Check pedigree information. | check.pedinfo |
| Score IBD state. | fgl2ibd |
| Score pairwise relatedness. | fgl2relatedness |
| Get pedigree index. | get.pedindex |
| GRM for multiple individuals | grm.matrix |
| GRM for a pair of individuals. | grm.pair |
| Score IBD length. | ibd.length |
| Score IBD sharing at a list of marker positions. | ibd.marker |
| Score IBD proportion. | ibd.proportion |
| Score IBD sharing by segment. | ibd.segment |
| LD weights | ld.weights |
| Populate SNPs. | populate.snp |
| Read PLINK binary file. | read.plink.binary |
| Read PLINK text file. | read.plink.text |
| Recode IBD sharing. | recode.ibd |
| Recode SNP marker data. | recode.snpdata |
| Simulate artificial haplotypes. | sim.haplotype |
| Simulate inheritance on a given pedigree. | sim.recomb |
| Write IBDHAPLO | write.ibdhaplo |
