Description Usage Arguments Value Examples
Simulate summary statistics according to the Han and Eskin's RE2 model. (Heterogeneity only when the population mean effect is non-zero)
1 2 | generate_data_re2(M = 50 * 10^3, p = 0.01, tau2 = 0.00025,
resref = NULL, n = rep(50 * 10^3, 10), I2 = 0.3)
|
M |
number of SNPs for which to simulate summary stats. |
p |
proportion of SNPs with real non-zero effects. |
tau2 |
variance of real associated non-zero SNPs. |
resref |
an optional vector of residual variances to sample from (with replacement) when generating the standard errors for the summary stats. Default is NULL, in which case the residual variances calculated from a Cigarretes Per Day GWAS (Liu, Jiang 2019) are used. |
n |
vector of sample sizes from the contributing studies. |
lambda |
proportion of NON-outlier studies for non-replicable SNPs. |
alpha |
variance inflation factor of outlier studies. |
A list containing:
An Mxk matrix of effect size estimates betajk
,
An Mxk matrix of effect size estimate variances sjk2
,
M-length vector inverse-variance weighted meta-analysis z-scores meta.z
,
an M-length binary vector indicating real / non-real effect at each SNP Rj
,
an M-length binary vector indicating true effect-size at each SNP muj
.
an Mxk matrix of the true study-level effects etajk
an M-length vector of the variance of the study-level effects around the SNP's population level effect omega2j
1 | generate_data_re2(M=100, p=0.01, tau2=2.5e-4, n=rep(10^4, 10), I2=0.2)
|
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