- joint_test.cpp
This is the c++ file that describes our main algorithm. Also included are the functions to run the variance component score test (that tests Genotype x Methylation x Tissue interaction effect)
- jaguar.cpp
This is the c++ file that describes JAGUAR, which is available at https://cran.r-project.org/web/packages/JAGUAR/index.html
- simulations_joint_test.R
This R script is necessary to run Monte Carlo simulations on our joint model.
- simulations_variance_comp_test.R
This R script runs Monte Carlo simulations comparing statistical power obtained from the variance component score test (for the Genotype x Methylation x Tissue interaction effect) with our joint model and for good measure, likelihoojd ratio test (RLRsim).
- simulations_JAGUAR_vs_JT.R
This R scripts runs Monte Carlo simulations comparing statistical power obtained from JAGUAR and our joint model both in the absence and presence of any effects due to methylation data.
- preprocess_gibbs.R
This R scripts preprocesses Gibbs et al adult human brain data from four brain regions, originally published at http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000952 This script essentially creates multiple sub-directories and deposits even partitions of gene expression and methylation data.
- run_joint_test.R
This R script runs our model on the Gibbs et al data fragments.
- run_separate_tbt.R
This R script runs a separate region-by-region analysis of gene expression and methylation data.
- run_TBT.R
This R script runs a region-by-region analysis using a linear model where methylation data is a covariate.
- run_vc_test.R
This R script runs a variance component score test to investigate any Genotype x Methylation x Tissue interaction effect in the Gibbs et al data.
- final_results.R
This script aggregates all the text files produced in each sub-directory after running all the above scripts and identifies statistically significant assocations.