RRate: Estimating Replication Rate in Genome-Wide Association Studies
About RRate |
Replication is a common validation method in GWAS. We regard an association as true finding when it shows significance in both the primary and replication studies. A worth pondering question is: what is the probability of a primary association (i.e. statistically
significant association in the primary study) being validated in the replication study? We propose a Bayesian probabilistic measure named Replication Rate (RR) to answer this question.
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Related Publication |
W. Jiang, J-H Xue and W. Yu "What is the probability of replicating a statistically significant association in genome-wide association studies? ", submitted. |
Where to download RRate |
The R-package is available at : |
Environment configuration |
It can be directly installed in the R environment with following command: |
Use the following command to load the package in the R environment: library("RRate") |
How to use it? |
The principal component of RRate package is repRateEst. Also we implement sample size determination method (repSampleSizeRR and repSampleSizeRR2) and consistency checking method (Hosmer-Lemeshow test, HLtest). |
Simulation Code |
Code: simulation_code.zip |
Simulation results |
$α_1=5× 10^{-8}$ and $α_2=5× 10^{-4}$: simulation_5e-4.zip |
Empirical results |
RR results for T2D data in DIAGRAM ($α_1=5× 10^{-8}$ and $α_2=5× 10^{-4}$): T2D-DIAGRAM_5e-4.zip |