The statgenGWAS package | Theoretical background | Application in the package | The class gData | Marker map | Marker matrix | Phenotypic data | Kinship matrix | Further covariates | Worked example | Load data | Create gData object | Recoding and cleaning of markers | Single trait GWAS | GWAS Summary | GWAS Plots | QQ-plots | Manhattan plots | QTL plots | Kinship matrices | Further options | Multiple trials and traits | Significance thresholds | Controlling false discovery rate | Variance covariance matrix | Genomic control correction | Covariates | Minor Allele Frequency | SNPs close to significant SNPs | References
Package: statgenGWAS 1.0.13
Bart-Jan van Rossum
statgenGWAS: Genome Wide Association Studies
Fast single trait Genome Wide Association Studies (GWAS) following the method described in Kang et al. (2010), <doi:10.1038/ng.548>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.
Authors:
statgenGWAS_1.0.13.tar.gz
statgenGWAS_1.0.13.zip(r-4.7)statgenGWAS_1.0.13.zip(r-4.6)statgenGWAS_1.0.13.zip(r-4.5)
statgenGWAS_1.0.13.tgz(r-4.6-x86_64)statgenGWAS_1.0.13.tgz(r-4.6-arm64)statgenGWAS_1.0.13.tgz(r-4.5-x86_64)statgenGWAS_1.0.13.tgz(r-4.5-arm64)
statgenGWAS_1.0.13.tar.gz(r-4.7-arm64)statgenGWAS_1.0.13.tar.gz(r-4.7-x86_64)statgenGWAS_1.0.13.tar.gz(r-4.6-arm64)statgenGWAS_1.0.13.tar.gz(r-4.6-x86_64)
statgenGWAS_1.0.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
statgenGWAS/json (API)
| # Install 'statgenGWAS' in R: |
| install.packages('statgenGWAS', repos = c('https://biometris.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/biometris/statgengwas/issues
Uses libs:
Datasets:
- dropsMap - DROPS data sets
- dropsMarkers - DROPS data sets
- dropsPheno - DROPS data sets
Last updated from:316cdc8d31. Checks:13 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 200 | ||
| linux-devel-x86_64 | OK | 210 | ||
| source / vignettes | OK | 301 | ||
| linux-release-arm64 | OK | 196 | ||
| linux-release-x86_64 | OK | 206 | ||
| macos-release-arm64 | OK | 123 | ||
| macos-release-x86_64 | OK | 376 | ||
| macos-oldrel-arm64 | OK | 115 | ||
| macos-oldrel-x86_64 | OK | 198 | ||
| windows-devel | OK | 162 | ||
| windows-release | OK | 182 | ||
| windows-oldrel | OK | 172 | ||
| wasm-release | OK | 198 |
Exports:codeMarkerscreateGDatakinshipreadPLINKreadVcfrunSingleTraitGwas
Dependencies:clicpp11crayondata.tabledotCall64enhancerfarverggplot2gluegtableisobandlabelinglatticelifecycleLMMsolverMASSMatrixR6RColorBrewerRcppRcppArmadilloRcppProgressrlangS7scalessommerspamvctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Code and impute markers | codeMarkers |
| DROPS data sets | dropsData dropsMap dropsMarkers dropsPheno |
| S3 Class gData | createGData gData |
| Functions for calculating kinship matrices | kinship |
| Plot function for the class 'gData' | plot.gData |
| Plot function for the class 'GWAS' | plot.GWAS |
| Read PLINK binary data | readPLINK |
| Read variant call format data | readVcf |
| Perform single-trait GWAS | runSingleTraitGwas |
| Summary function for the class 'gData' | summary.gData |
| Summary function for the class 'GWAS' | summary.GWAS |
