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.

What is in the package?

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

Included Functionality

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.

Installation

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")

Citing this package

For citing this package, please use the following source:

citation("gnonadd")
#> 
#> To cite gnonadd in publications, please use
#> 
#>   Snaebjarnarson, Audunn S., et al. Complex effects of sequence
#>   variants on lipid levels and coronary artery disease. Cell 186.19
#>   (2023): 4085-4099.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     journal = {Cell},
#>     volume = {186},
#>     number = {19},
#>     pages = {4085--4099},
#>     year = {2023},
#>     author = {{Snaebjarnarson} and Audunn S and {Helgadottir} and {Anna} and {Arnadottir} and Gudny A and {Ivarsdottir} and Erna V and {Thorleifsson} and {Gudmar} and {Ferkingstad} and {Egil} and {Einarsson} and {Gudmundur} and {Sveinbjornsson} and {Gardar} and {Thorgeirsson} and Thorgeir E and {Ulfarsson} and Magnus O and others},
#>     title = {Complex effects of sequence variants on lipid levels and coronary artery disease},
#>     publisher = {Elsevier},
#>   }