This repository contains code and data accompanying the upcoming publication "Exploring the function of the BBSome using clinical data: Meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome"

Contents of the files:

• data folder, contains the main dataset and results of the frequentist analyses from the main manuscript
• main_analysis.Rmd describes (both in accessible and a mathy way) the model reported in the main manuscript. Reproduces all of the Bayesian figures from the main manscript + some additional checks and insights
• alternative_models.Rmd describes all alternative models we tried throughout the analysis and shows posterior predictive checks that guided our selection of the model for the main analysis
• multiverse_analysis.Rmd compares how the main conclusions of the paper hold under all alternative models, both Bayesian and frequentist.
• validation_dataset.Rmd code made to validate the findings on new data. We were later denied access to new data and the code here is discontinued.
• master_document.Rmd includes the 3 Rmd files above to form a single document for journal submissions
• master_document_with_validation.Rmd an alternative to mater_document.Rmd also including validation. Discontinued after we were denied access to the new dataset.
• data_processing.R code to load and preprocess the dataset
• models.R definitions of all models used in the analysis
• models_funcs.R helper functions to easily fit the dataset with all models
• plots.R code for all the fancy plots used in the analysis

To rerun, you need to install brms whic requires rstan. Installing rstan directly with install.package may fail on some systems - see https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started for more details.

The model fitting for the analyses may be time consuming. To avoid recomputing, fits are stored in the stored_fits directory, which is created on the fly. To save you time refitting, you can download the fits we used at: https://zenodo.org/record/3243270 (DOI: 10.5281/zenodo.3243270). Downloading the fits should also let you rerun the code without completely configuring rstan.

You can rerun the complete analysis be knitting master_document.Rmd, but the individual parts can also be executed/knitted separately.

main_analysis.Rmd is self-sufficient and can be run directly. It fits the main model, which should be relatively quick (20min - 1 hour).

alternative_models.Rmd is self-sufficient and can be run directly. This will fit a large number of relatively large models and may take upwards of a day even on a powerful machine.

To run multiverse_analysis.Rmd you need to run alternative_models.Rmd first (or download fitted models), but after that it is pretty quick.