gaawr2
Genetic Association Analysis
This is a companion to Henry-Stewart talk by Zhao (2026, <doi:10.69645/FRFQ9519>), which gathers information, metadata and scripts to showcase modern genetic analysis -- ranging from testing of polymorphic variant(s) for Hardy-Weinberg equilibrium, association with traits using genetic and statistical models, Bayesian implementation, power calculation in study design, and genetic annotation. It also covers R integration with the Linux environment, GitHub, package creation and web applications. The earlier version by Zhao (2009, <doi:10.69645/DCRY5578>) provides a brief introduction to these topics.
README
# A summary of files Filename | Description -----------|-------------------------------- biomaRt.R | biomaRt query cran.sh* | CRAN package extraction docs.sh* | GitHub updates ens.R | Ensembl database gaawr2.R | R/**gaawr2** creation github.sh* | GitHub/**gaawr2** creation GMMAT.R | **GMMAT** script h2.jags.R | h2.jags documentation example haplo.stats.R | **haplo.stats** script HardyWeinberg.R | **HardyWeinberg** scrip hello.R | "Hello, world!" httr.R | **httr** script lz.R | **locuszoomr** script ontologyIndex.R | **ontologyIndex** script OpenTargets.R | OpenTarget query pkgdown.sh*| **pkgdown** script powerEQTL.R| **powerEQTL** script README.md | This file rentrez.R | **entrez** query SNPassoc.R | **SNPassoc** script tabix.sh* | **tabix** script Given the limited allowance for computing time for CRAN checking, scripts here are largely perferable to those in the package vignette, [`gaawr2`]. Owing to CRAN poly, R scripts are revised to be functions. Additionally, - `cran.sh` makes a copy of the latest repository but drops files not needed by CRAN. - `hwe_ternary_plotly.py` is a Python script using plotly for the HWE ternary plot whose top vertex (the “a‑axis”) represents A1A2, the left vertex (the “b‑axis”) A1A2, and the right vertex (the “c‑axis”) A2A2.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.0.7 |
rolling linux/jammy R-4.5 | gaawr2_0.0.7.tar.gz |
968.5 KiB |
0.0.7 |
rolling linux/noble R-4.5 | gaawr2_0.0.7.tar.gz |
968.4 KiB |
0.0.7 |
rolling source/ R- | gaawr2_0.0.7.tar.gz |
1.2 MiB |
0.0.7 |
latest linux/jammy R-4.5 | gaawr2_0.0.7.tar.gz |
968.5 KiB |
0.0.7 |
latest linux/noble R-4.5 | gaawr2_0.0.7.tar.gz |
968.4 KiB |
0.0.7 |
latest source/ R- | gaawr2_0.0.7.tar.gz |
1.2 MiB |
0.0.7 |
2026-04-26 source/ R- | gaawr2_0.0.7.tar.gz |
1.2 MiB |
0.0.7 |
2026-04-23 source/ R- | gaawr2_0.0.7.tar.gz |
1.2 MiB |
0.0.7 |
2026-04-09 windows/windows R-4.5 | gaawr2_0.0.7.zip |
977.1 KiB |
0.0.3 |
2025-04-20 source/ R- | gaawr2_0.0.3.tar.gz |
442.8 KiB |