README.md
In gnonadd: Various Non-Additive Models for Genetic Associations

gnonadd

gnonadd is a package accompanying the paper Complex effects of sequence variants on lipid levels and coronary artery disease published in Cell September 2023. The package is intended to properly document the conducted analysis and aid researchers in studying various non-additive models.

The goal of the gnonadd package is to simplify workflows with non-additive analysis in genetic associations.

This includes e.g.

1) Variance effects 2) Correlation effects 3) Interaction effects 4) Dominance effects

The following is a non-comprehensive summary of the included functions:

alpha.calc function to compute multiplicative variance effects
alpha.cond function to do conditional analysis of variance effects
kappa_calc function to compute correlation effects (gt/pheno/pheno)
Correlation calibration
Var.assoc Testing variance scores associations with data
Dominance effect model implementation
Interaction effect model (gt/gt/pheno) (genotype interaction) implementation
Pairwise genotype interaction implementation for list of genotypes
Interaction effect model (gt/pheno/pheno) (environment interaction) implementation
Environment interaction cross of lists of phenotypes and genotypes (single outcome phenotype)
Function to create traditional genetic score
Function to create traditional genetic score with interaction effects as well
Function to create traditional genetic score with interaction effects and dominance effects as well
Function to create variance genetic score
Summary visualizations
Histograms by genotype

Please refer to the documentation for examples with simulated data.

You can install the latest version of the package via the remotes package:

# Use remotes:
remotes::install_github("DecodeGenetics/gnonadd")

The current version on CRAN can be installed with:

install.packages("gnonadd")

For citing this package, please use the following source:

citation("gnonadd")
#> 
#> To cite gnonadd in publications use:
#> 
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {Complex effects of sequence variants on lipid levels and coronary artery disease},
#>     author = {Audunn S. Snaebjarnarson et al.},
#>     journal = {Cell},
#>     year = {2023},
#>     volume = {186},
#>     issue = {19},
#>     pages = {4085-4099.e15},
#>     url = {https://www.sciencedirect.com/science/article/pii/S0092867423009017},
#>     doi = {https://doi.org/10.1016/j.cell.2023.08.012},
#>   }