simplePHENOTYPES: Simulation of Pleiotropic, Linked and Epistatic Phenotypes

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 ORCID iD [aut, cre], Alexander Lipka ORCID iD [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

Downloads:

Reference manual: simplePHENOTYPES.pdf
Vignettes: Introduction to simplePHENOTYPES
Package source: simplePHENOTYPES_1.0.5.tar.gz
Windows binaries: r-devel: simplePHENOTYPES_1.0.5.zip, r-devel-gcc8: simplePHENOTYPES_1.0.5.zip, r-release: simplePHENOTYPES_1.0.5.zip, r-oldrel: simplePHENOTYPES_1.0.5.zip
OS X binaries: r-release: simplePHENOTYPES_1.0.5.tgz, r-oldrel: simplePHENOTYPES_1.0.5.tgz

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