smryStats: Example summary statistics
In RRate: Estimating Replication Rate for Genome-Wide Association Studies

Description Usage Details Author(s) References See Also

Example summary statistics from the primary and replication studies in GWAS. These summary statistics are generated from a simulated study. The primary study (smryStats1) has 2000 cases and 2000 controls. The replication study (smryStats2) has 1000 cases and 1000 controls. The SNP number is 10,000. The disease pravalence is 1%. Minor allele frequencies are from U(0.05, 0.5), and log-odds ratio are from 0.95N(0,1)+0.05N(0, 0.04). The ground-truth parameters for each SNP are in param.

data(smryStats1)

data(smryStats2)

data(param)

The data sets are described as

SNP: SNP ID

F_A: Allele frequency in case group

F_U: Allele frequency in control group

Z: Z value from log-odds ratio test

P: P value

OR: Odds ratio

SE: Standard error of log(OR)

Wei Jiang, Jing-Hao Xue and Weichuan Yu

Maintainer: Wei Jiang <wjiangaa@connect.ust.hk>

Jiang, W., Xue, J-H, and Yu, W. What is the probability of replicating a statistically significant association in genome-wide association studies?. Submitted.

RRate repRateEst, SEest, repSampleSizeRR, repSampleSizeRR2, HLtest