[aut, cre],
Alexander Lipka
[aut]The number of studies involving correlated traits and the availability of tools to handle this type of data has increased considerably in the last decade. With such a demand, we need tools for testing hypotheses related to single and multi-trait (correlated) phenotypes based on many genetic settings. Thus, we implemented various options for simulation of pleiotropy and Linkage Disequilibrium under additive, dominance and epistatic models. The simulation currently takes a HapMap file as an input and numericalize it with GAPIT.numericalization Lipka et al. (2012) <doi:10.1093/bioinformatics/bts444>. The numericalized dataset is then used by a framework adapted from Rice and Lipka (2019) <doi:10.3835/plantgenome2018.07.0052> for simulating multiple traits.
| Version: | 1.0.5 |
| Depends: | R (≥ 3.5.0) |
| Imports: | data.table, mvtnorm, lqmm, stats, utils, SNPRelate, gdsfmt |
| Suggests: | knitr, rmarkdown |
| Published: | 2019-12-04 |
| Author: | Samuel Fernandes
[aut, cre],
Alexander Lipka
[aut] |
| Maintainer: | Samuel Fernandes <samuelf at illinois.edu> |
| BugReports: | https://github.com/samuelbfernandes/simplePHENOTYPES/issues |
| License: | MIT + file LICENSE |
| URL: | https://github.com/samuelbfernandes/simplePHENOTYPES |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | simplePHENOTYPES results |
| Reference manual: | simplePHENOTYPES.pdf |
| Vignettes: |
Introduction to simplePHENOTYPES |
| Package source: | simplePHENOTYPES_1.0.5.tar.gz |
| Windows binaries: | r-prerelease: simplePHENOTYPES_1.0.5.zip, r-release: simplePHENOTYPES_1.0.5.zip, r-oldrel: simplePHENOTYPES_1.0.5.zip |
| macOS binaries: | r-prerelease: not available, r-release: simplePHENOTYPES_1.0.5.tgz, r-oldrel: simplePHENOTYPES_1.0.5.tgz |
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