Summary statistics are generated by simulating individual-level genotype and phenotype data followed by association analysis by linear regression.
Located in folder individual_level_simulations
:
bal_InSIDE_simulate_beta.R
: Individual-level simulations under balanced pleiotropy and InSIDE assumption satisfied.bal_noInSIDE_simulate_beta.R
: Individual-level simulations under balanced pleiotropy and InSIDE assumption violated.merge_individual_betahat.R
: Merge data from all simulation groups.MR_analysis.R
: Conduct MR analysis on simulated summary statistics.
Summary statistics are simulated directly from the summary-level model implied by the individual-level model without generating individual genotype and phenotype data. Summary level simulations are substantially faster than individual-level simulations.
Located in folder summary_level_simualtions
:
bal_InSIDE_smry.R
: Summary-level simulations under balanced pleiotropy and InSIDE assumption satisfied.bal_noInSIDE_smry.R
: Summary-level simulations under balanced pleiotropy and InSIDE assumption violated.dir_InSIDE_smry.R
: Summary-level simulations under directional pleiotropy and InSIDE assumption satisfied.dir_noInSIDE_smry.R
: Summary-level simulations under directional pleiotropy and InSIDE assumption violated.
MR_lasso.R
: function to implement MR-Lasso, obtained from the following paper:
Slob, Eric AW, and Stephen Burgess. "A Comparison Of Robust Mendelian Randomization Methods Using Summary Data." BioRxiv (2019): 577940.