Overview
RyouSick is an R package designed to simulate both small and large data sets containing genotype and phenotype information on individuals (read more in vignette("Simulation_Basis")). It furthermore provides tools to analyse such datasets to find out which genetic compositions might cause various inherited disorders (read more in the articles vignette("GWAS"), vignette("GWAX") and vignette("LTFH")).
As such, RyouSick provides a dual functionality. Firstly, users will be able input real genotype and phenotype data, provided that it is correctly formatted and loaded (See more on the “Get Started” page and the article vignette("Writing_efficient_R_code_and_working_with_large_datasets")), and analyze it using one of the provided analysis methods to find out which SNPs might be causing a disorder. The output of the analysis can then be passed on to the prediction function provided in the package (read more in vignette("Prediction")), which will generate a model than can be used to predict the disease status of future genotype cases.
Secondly, users can simulate genetic data using the in-package functions and perform their own analysis on it and then compare their performance with more established analysis methods that are provided in the package.
Reading the articles in the presented order will present an introduction to the subject matter, but if you are just dying to begin using the package, head over to the “Get Started” page to dive right into RyouSick and its functionalities.
Installation
You can install the development version of RyouSick from GitHub with:
# install.packages("devtools") if devtools not already installed
devtools::install_github("Best-Nicklas/Dataprojekt")Dependencies
To store large quantities of data outside the RAM and perform calculations on this data, RyouSick uses the bigsnpr and bigstatr packages. Additionally RyouSick allows speedup of simulations by the use of parallelization which is underpinned by the future.apply package and the future backend. Besides these, a number of tidyverse packages, such tibble, dplyr and purrr are used in the package and will, together with the aformentioned packages, also be installed along with RyouSick.