Package: GWASpoly 2.13
Jeffrey Endelman
GWASpoly: Genome-wide Association Studies for Autopolyploids
Designed for genome-wide association studies in autopolyploids.
Authors:
GWASpoly_2.13.tar.gz
GWASpoly_2.13.zip(r-4.5)GWASpoly_2.13.zip(r-4.4)GWASpoly_2.13.zip(r-4.3)
GWASpoly_2.13.tgz(r-4.4-any)GWASpoly_2.13.tgz(r-4.3-any)
GWASpoly_2.13.tar.gz(r-4.5-noble)GWASpoly_2.13.tar.gz(r-4.4-noble)
GWASpoly_2.13.tgz(r-4.4-emscripten)GWASpoly_2.13.tgz(r-4.3-emscripten)
GWASpoly.pdf |GWASpoly.html✨
GWASpoly/json (API)
NEWS
| # Install 'GWASpoly' in R: |
| install.packages('GWASpoly', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jendelman/gwaspoly/issues
Last updated 1 years agofrom:c8c80a5ec5
Exports:fit.QTLget.QTLGWASpolyLD.plotmanhattan.plotqq.plotread.GWASpolyset.Kset.paramsset.thresholdVCF2dosagewrite.GWASpoly
Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6randomForestRColorBrewerrlangrrBLUPscalesscamstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Test markers as QTL under backward elimination | fit.QTL |
| Extract significant QTL | get.QTL |
| Compute marker significance scores | GWASpoly |
| S4 class with genotype and phenotype data | GWASpoly.data GWASpoly.data-class |
| S4 class with results from genome-wide scan | GWASpoly.fitted GWASpoly.fitted-class |
| S4 class with genotypes, phenotypes, and polygenic covariance | GWASpoly.K GWASpoly.K-class |
| S4 class with results from genome-wide scan and detection threshold | GWASpoly.thresh GWASpoly.thresh-class |
| Plot LD vs distance | LD.plot |
| Create Manhattan plot | manhattan.plot |
| Quantile-Quantile (QQ) Plot | qq.plot |
| Read in marker and phenotype data | read.GWASpoly |
| Set covariance matrix for polygenic effect | set.K |
| Set parameters | set.params |
| Set the significance threshold | set.threshold |
| Convert VCF to dosage file | VCF2dosage |
| Write results to file | write.GWASpoly |
