\(\hat\pi_0\) on correlated global null estimated by ashr and truncash

Introduction

Using correlated global null data simulated from GTEx/Liver, \(\hat\pi_0\) is estimated by truncash and ashr. Ideally the estimates should be close to \(1\).

Simulation

In truncash, the threshold is \(T = 1.96\).

library(ashr)
source("../code/truncash.R")

p = read.table("../output/p_null_liver_777.txt")
z = read.table("../output/z_null_liver_777.txt")
betahat = read.table("../output/betahat_null_liver_777.txt")

m = dim(p)[1]
n = dim(p)[2]
pihat0.ash = pihat0.truncash = c()

for (i in 1:m) {
  betahat_trial = as.numeric(betahat[i, ])
  sebetahat_trial = - betahat_trial / as.numeric(z[i, ])
  fit.ash = ashr::ash(betahat_trial, sebetahat_trial, method = "fdr", mixcompdist = "normal")
  pihat0.ash[i] = get_pi0(fit.ash)
  fit.truncash = truncash(betahat_trial, sebetahat_trial, t = qnorm(0.975))
  pihat0.truncash[i] = get_pi0(fit.truncash)
}

Result

False positive rate by ash

mean(pihat0.ash < 1)

[1] 0.287

False positive rate by truncash

mean(pihat0.truncash < 1)

[1] 0.202

Compare \(\hat\pi_0\) estimated by ash and truncash

xlim = c(min(c(pihat0.ash, pihat0.truncash)), 1)
plot(pihat0.ash, pihat0.truncash, xlim = xlim, ylim = xlim, xlab = "ash", ylab = "truncash", main = expression(hat(pi)[0]))
abline(0, 1, lty = 2, col = "blue")
abline(v = 1, lty = 3, col = "red")
abline(h = 1, lty = 3, col = "red")

boxplot(pihat0.ash, pihat0.truncash, main = expression(hat(pi)[0]), names = c("ash", "truncash"))
abline(h = 1, lty = 2, col = "red")

Session Information

sessionInfo()

R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.3

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] SQUAREM_2016.10-1 ashr_2.1.2       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.9       knitr_1.15.1      magrittr_1.5     
 [4] workflowr_0.3.0   MASS_7.3-45       doParallel_1.0.10
 [7] pscl_1.4.9        lattice_0.20-34   foreach_1.4.3    
[10] stringr_1.1.0     tools_3.3.2       parallel_3.3.2   
[13] grid_3.3.2        git2r_0.18.0      htmltools_0.3.5  
[16] iterators_1.0.8   yaml_2.1.14       rprojroot_1.2    
[19] digest_0.6.9      codetools_0.2-15  evaluate_0.10    
[22] rmarkdown_1.3     stringi_1.1.2     backports_1.0.5  
[25] truncnorm_1.0-7