RRate-functions {RRate} | R Documentation |
Estimating Replication Rate for primary associations
Description
repRateEst
implements a replication rate estimation method. Two-component mixture prior is used in the estimation.
Usage
repRateEst(MUhat, SE, SE2, zalpha2, zalphaR2, boot = 100, output = TRUE,
idx = TRUE, dir = "output", info = TRUE)
Arguments
MUhat |
The observed effect size (log-odds ratio) in the primary study. |
SE |
The standard error of the observed log-odds ratio in the primary study. |
SE2 |
The standard error of the observed log-odds ratio in the replication study. |
zalpha2 |
The critical value of z-values in the primary study, i.e. z_alpha/2. |
zalphaR2 |
The critical value of z-values in the replication study, i.e. z_alphaR/2. |
boot |
The resampling number of bootstrop used for estimating the credible interval of the RR. |
output |
Bool value. To determine whether to output the estimated results in the dir or not. |
idx |
The indexes of the SNPs having been further inverstigated in the replication study. We only calculate RR for primary associations with indexes in |
dir |
The directory to save the estimated results. It has effect when |
info |
Bool value. To determine whether to show the parematers inference results in the terminal or not. |
Details
The RR estimation is based on the following two-component mixture model: mu=pi_0 delta_0+(1-pi_0) N(0, sigma_0^2).
Details can be seen the following reference paper.
Value
repRateEst
returns the RR, lfdr, prediction power and infered parameters. The returened value is a LIST:
idx |
The index of the SNPs which RR are estimated. |
pi0 |
The proportion of nonassociated SNPs. |
sigma02 |
The variance of the associated SNPs' effect sizes |
RR |
Estimated replication rate. |
RRlow |
The lower limit of the 95% CI for RR. |
RRhigh |
The upper limit of the 95% CI for RR. |
lfdr |
Estimated local false discovery rate of the primary study |
lfdrLow |
The lower limit of the 95% CI for lfdr. |
lfdrHigh |
The upper limit of the 95% CI for lfdr. |
predPower |
The Bayesian predictive power of the replication study. |
predPowerLow |
The lower limit of the 95% CI for predPower. |
perdPowerHigh |
The upper limit of the 95% CI for predPower. |
GRR |
The Global Replication Rate (Mean value of RR) |
GRRlow |
The lower limit of the 95% CI for GRR. |
GRRhigh |
The upper limit of the 95% CI for GRR. |
Author(s)
Wei Jiang, Jing-Hao Xue and Weichuan Yu
Maintainer: Wei Jiang <wjiangaa@connect.ust.hk>
References
Jiang, W., Xue, J-H, and Yu, W. What is the probability of replicating a statistically significant association in genome-wide association studies?. Submitted.
See Also
RRate
,
SEest
,
repSampleSizeRR
,
repSampleSizeRR2
,
HLtest
Examples
alpha<-5e-6 #Significance level in the primary study
alphaR<-5e-3 #Significance level in the replication study
zalpha2<-qnorm(1-alpha/2)
zalphaR2<-qnorm(1-alphaR/2)
##Load data
data('smryStats1') #Example of summary statistics in 1st study
n2.0<-2000 #Number of individuals in control group
n2.1<-2000 #Number of individuals in case group
SE2<-SEest(n2.0, n2.1, smryStats1$F_U, smryStats1$F_A) #SE in replication study
###### RR estimation ######
RRresult<-repRateEst(log(smryStats1$OR),smryStats1$SE, SE2,zalpha2,zalphaR2, output=TRUE,dir='.')
RR<-RRresult$RR #Estimated RR