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 marker data set as an input and then uses it for simulating multiple traits as described in Fernandes and Lipka (2020) <doi:10.1186/s12859-020-03804-y>.

Version:	1.3.0
Depends:	R (≥ 3.5.0)
Imports:	data.table, mvtnorm, stats, utils, SNPRelate, gdsfmt
Suggests:	knitr, rmarkdown
Published:	2021-01-20
DOI:	10.32614/CRAN.package.simplePHENOTYPES
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
Citation:	simplePHENOTYPES citation info
Materials:	README, NEWS
In views:	Agriculture
CRAN checks:	simplePHENOTYPES results

Documentation:

Reference manual:	simplePHENOTYPES.html , simplePHENOTYPES.pdf
Vignettes:	Introduction to simplePHENOTYPES (source, R code)

Downloads:

Package source:	simplePHENOTYPES_1.3.0.tar.gz
Windows binaries:	r-devel: simplePHENOTYPES_1.3.0.zip, r-release: simplePHENOTYPES_1.3.0.zip, r-oldrel: simplePHENOTYPES_1.3.0.zip
macOS binaries:	r-release (arm64): simplePHENOTYPES_1.3.0.tgz, r-oldrel (arm64): simplePHENOTYPES_1.3.0.tgz, r-release (x86_64): simplePHENOTYPES_1.3.0.tgz, r-oldrel (x86_64): simplePHENOTYPES_1.3.0.tgz
Old sources:	simplePHENOTYPES archive

Linking:

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