Last updated: 2019-02-24

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    Rmd 2fe3a41 zouyuxin 2019-02-24 wflow_publish(“analysis/SuSiEzRProblem42.Rmd”)

The simulated data has 5 true effects. The PVE is 0.8.

library(susieR)
X = readRDS('output/small_data_42.rds')$X
data = readRDS('output/small_data_42_sim_gaussian_36.rds')
sumstats = readRDS('output/small_data_42_sim_gaussian_36_get_sumstats_2.rds')
Y = data$Y
beta = data$meta$true_coef
z = sumstats$sumstats$bhat/sumstats$sumstats$shat
susie_plot(z, y = "z", b=beta)

The true signals are 202, 266, 373, 573, 907.

The estimated residual variance becomes negative in SuSiE z.

The result from FINEMAP does not look well: FINEMAP result.

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.3

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] susieR_0.6.4.0438

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_1.0.0        lattice_0.20-38  
 [4] digest_0.6.18     rprojroot_1.3-2   R.methodsS3_1.7.1
 [7] grid_3.5.1        backports_1.1.3   git2r_0.24.0     
[10] magrittr_1.5      evaluate_0.12     stringi_1.2.4    
[13] whisker_0.3-2     R.oo_1.22.0       R.utils_2.7.0    
[16] Matrix_1.2-15     rmarkdown_1.11    tools_3.5.1      
[19] stringr_1.3.1     yaml_2.2.0        compiler_3.5.1   
[22] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1