Description
Various Non-Additive Models for Genetic Associations
Description
The goal of 'gnonadd' is to simplify workflows in the analysis of non-additive effects of sequence variants. This includes variance effects (Ivarsdottir et. al (2017) <doi:10.1038/ng.3928>), correlation effects, interaction effects and dominance effects. The package also includes convenience functions for visualization.
README.md
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.
- Variance effects
- Correlation effects
- Interaction effects
- Dominance effects
Included Functionality
The following is a non-comprehensive summary of the included functions:
alpha.calc
function to compute multiplicative variance effectsalpha.cond
function to do conditional analysis of variance effectskappa_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 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},
#> }