simtrait: Simulate Complex Traits from Genotypes

Simulate complex traits given a SNP genotype matrix and model parameters (the desired heritability, number of causal loci, and either the true ancestral allele frequencies used to generate the genotypes or the mean kinship for a real dataset). Emphasis on avoiding common biases due to the use of estimated allele frequencies. The code selects random loci to be causal, constructs coefficients for these loci and random independent non-genetic effects. Traits can follow three models: random coefficients, fixed effect sizes, and infinitesimal (multivariate normal). GWAS method benchmarking functions are also provided. Partially described in Yao and Ochoa (2019) <doi:10.1101/858399>.

Version:	1.0.21
Imports:	PRROC
Suggests:	popkin, testthat, knitr, rmarkdown, bnpsd, BEDMatrix
Published:	2021-08-16
Author:	Alejandro Ochoa [aut, cre]
Maintainer:	Alejandro Ochoa <alejandro.ochoa at duke.edu>
BugReports:	https://github.com/OchoaLab/simtrait/issues
License:	GPL-3
URL:	https://github.com/OchoaLab/simtrait
NeedsCompilation:	no
Materials:	README NEWS
CRAN checks:	simtrait results

Documentation:

Reference manual:	simtrait.pdf
Vignettes:	'simtrait': Simulate Complex Traits from Genotypes

Downloads:

Package source:	simtrait_1.0.21.tar.gz
Windows binaries:	r-devel: simtrait_1.0.21.zip, r-release: simtrait_1.0.21.zip, r-oldrel: simtrait_1.0.21.zip
macOS binaries:	r-release (arm64): simtrait_1.0.21.tgz, r-oldrel (arm64): simtrait_1.0.21.tgz, r-release (x86_64): simtrait_1.0.21.tgz, r-oldrel (x86_64): simtrait_1.0.21.tgz

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