Last updated: 2017-05-12

Code version: fd54c84

library(ashr)
set.seed(777)
x = rnorm(100)
qqnorm(x)
qqline(x)

y = runif(100)
qqnorm(y)
qqline(y)

beta = runif(10000)
betahat = beta + rnorm(10000)
fit = ash(betahat, 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit)

Press [enter] to see next plot

Press [enter] to see next plot

Press [enter] to see next plot

par(mfrow = c(2, 2))
fit = ash(rnorm(10000), 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit, breaks = 100)
Press [enter] to see next plot
Press [enter] to see next plot
Press [enter] to see next plot

beta = sample(c(rnorm(5000, 1.5, 1), rnorm(5000, -1.5, 1)))
betahat = beta + rnorm(10000)
fit = ash(betahat, 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit, breaks = 100)
Press [enter] to see next plot
Press [enter] to see next plot
Press [enter] to see next plot

z = readRDS("../output/z_null_liver_777_select.RDS")
z = z$typical[[5]]
hist(z, breaks = 100, prob = TRUE, xlab = "Correlated N(0, 1) Z Scores", ylim = c(0, dnorm(0)), main = "Histogram of Correlated Z Scores")
lines(seq(-6, 6, 0.01), dnorm(seq(-6, 6, 0.01)), col = "red")

hist(z, breaks = 100, prob = TRUE, xlab = "Correlated N(0, 1) Z Scores", ylim = c(0, 0.1), main = "Histogram of Correlated Z Scores: Left Tail", xlim = c(-5, -2.5))
lines(seq(-6, 6, 0.01), dnorm(seq(-6, 6, 0.01)), col = "red")

library(ashr)
fit = ashr::ash(z, 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit, breaks = 100)

Press [enter] to see next plot

Press [enter] to see next plot

Press [enter] to see next plot

Session information

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12.4

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] ashr_2.1-10

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.10      knitr_1.15.1      magrittr_1.5     
 [4] REBayes_0.62      MASS_7.3-45       doParallel_1.0.10
 [7] pscl_1.4.9        SQUAREM_2016.10-1 lattice_0.20-34  
[10] foreach_1.4.3     stringr_1.2.0     tools_3.3.3      
[13] parallel_3.3.3    grid_3.3.3        git2r_0.18.0     
[16] htmltools_0.3.5   iterators_1.0.8   assertthat_0.1   
[19] yaml_2.1.14       rprojroot_1.2     digest_0.6.11    
[22] Matrix_1.2-8      codetools_0.2-15  evaluate_0.10    
[25] rmarkdown_1.3     stringi_1.1.2     Rmosek_7.1.3     
[28] backports_1.0.5   truncnorm_1.0-7

This R Markdown site was created with workflowr