RRate: Estimating Replication Rate in GenomeWide 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.

Related Publication 
W. Jiang, JH Xue and W. Yu "What is the probability of replicating a statistically significant association in genomewide association studies? ", submitted. 
Where to download RRate 
The Rpackage 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 (HosmerLemeshow test, HLtest). 
Simulation Code 
Code: simulation_code.zip 
Simulation results 
$α_1=5× 10^{8}$ and $α_2=5× 10^{4}$: simulation_5e4.zip 
Empirical results 
RR results for T2D data in DIAGRAM ($α_1=5× 10^{8}$ and $α_2=5× 10^{4}$): T2DDIAGRAM_5e4.zip 