plot_diagnostic
in ashr
Last updated: 2017-12-21
Code version: 6e42447
This file documents some simulations done for a May 12, 2017, NHS presentation on the diagnostic plots for ASH implemented by ashr::plot_diagnostic()
.
library(ashr)
library(qvalue)
set.seed(777)
x = rnorm(100)
qqnorm(x)
qqline(x)
y = runif(100)
qqnorm(y)
qqline(y)
ASH
applied to different data setsbeta = runif(10000)
betahat = beta + rnorm(10000)
fit = ash(betahat, 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit)
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par(mfrow = c(2, 2))
fit = ash(rnorm(10000), 1, mixcompdist = "normal", method = "fdr")
plot_diagnostic(fit, breaks = 100)
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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)
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sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.2
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
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] qvalue_2.10.0 ashr_2.2-2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.14 compiler_3.4.3 git2r_0.20.0
[4] plyr_1.8.4 iterators_1.0.9 tools_3.4.3
[7] digest_0.6.13 evaluate_0.10.1 tibble_1.3.4
[10] gtable_0.2.0 lattice_0.20-35 rlang_0.1.4
[13] Matrix_1.2-12 foreach_1.4.4 yaml_2.1.16
[16] parallel_3.4.3 stringr_1.2.0 knitr_1.17
[19] REBayes_1.2 rprojroot_1.3-1 grid_3.4.3
[22] rmarkdown_1.8 ggplot2_2.2.1 reshape2_1.4.3
[25] magrittr_1.5 backports_1.1.2 scales_0.5.0
[28] codetools_0.2-15 htmltools_0.3.6 MASS_7.3-47
[31] splines_3.4.3 assertthat_0.2.0 colorspace_1.3-2
[34] stringi_1.1.6 Rmosek_8.0.69 lazyeval_0.2.1
[37] pscl_1.5.2 doParallel_1.0.11 munsell_0.4.3
[40] truncnorm_1.0-7 SQUAREM_2017.10-1
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