Last updated: 2019-01-23

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Unstaged changes:
    Modified:   analysis/EstimateCorMaxMVSample.Rmd
    Modified:   analysis/Mash_UKBio.Rmd
    Modified:   analysis/WASPmash.Rmd
    Modified:   analysis/mash_missing_samplesize.Rmd
    Modified:   output/Flash_T2_0.rds
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    File Version Author Date Message
    Rmd 6353efc zouyuxin 2019-01-23 wflow_publish(“analysis/EstimateCorNullProblem.Rmd”) 

library(mashr)
Loading required package: ashr
library(mvtnorm)
library(knitr)
library(kableExtra)

We simulate 1000 data from \[ \hat{b}|b \sim N_{5}(\hat{b}; b, \left(\begin{matrix} 1 & & 0.3 & &\\ & & \ddots & \\ & & 0.3 & & 1 \end{matrix}\right)) \]

\[ b \sim \delta_{0} \]

\(\Rightarrow\) \[ \hat{b} \sim N_{5}(0, \left(\begin{matrix} 1 & & 0.3 & &\\ & & \ddots & \\ & & 0.3 & & 1 \end{matrix}\right)) \]

set.seed(1)
n = 1000; p = 5
Sigma = matrix(0.3, p,p)
diag(Sigma) = 1
B = matrix(0,n,p)
Bhat = rmvnorm(n, sigma = Sigma)
simdata = list(B = B, Bhat = Bhat, Shat = 1)
data = mash_set_data(Bhat, Shat=1)
U.c = cov_canonical(data)
m.ignore = mash(data, U.c, verbose = FALSE, optmethod = 'mixSQP')

V.simple = estimate_null_correlation_simple(data)
data.simple = mash_update_data(data, V = V.simple)
m.simple = mash(data.simple, U.c, verbose = FALSE, optmethod = 'mixSQP')

V.current = estimate_null_correlation(data, Ulist = U.c)
m.current = V.current$mash.model

data.true = mash_update_data(data, V = Sigma)
m.true = mash(data.true, U.c, verbose = FALSE, optmethod = 'mixSQP')
ign = c(get_loglik(m.ignore), length(get_significant_results(m.ignore)))

simple = c(get_loglik(m.simple), length(get_significant_results(m.simple)))

current = c(get_loglik(m.current), length(get_significant_results(m.current)))

true = c(get_loglik(m.true), length(get_significant_results(m.true)))

tmp = rbind(ign, simple, current, true)
row.names(tmp) = c('ignore', 'simple', 'current', 'true')
colnames(tmp) = c('loglik', '# signif')
tmp %>% kable() %>% kable_styling()
loglik # signif
ignore -7000.556 59
simple -6913.520 0
current -6905.050 0
true -6908.123 0 
par(mfrow= c(1,2))
barplot(get_estimated_pi(m.ignore), las=2, cex.names = 0.7, main='Ignore')
barplot(get_estimated_pi(m.true), las=2, cex.names = 0.7, main='True')

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.2

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] kableExtra_1.0.1  knitr_1.20        mvtnorm_1.0-8     mashr_0.2.19.0555
[5] ashr_2.2-26      

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0        highr_0.7         pillar_1.3.1     
 [4] compiler_3.5.1    git2r_0.24.0      plyr_1.8.4       
 [7] workflowr_1.1.1   R.methodsS3_1.7.1 R.utils_2.7.0    
[10] iterators_1.0.10  tools_3.5.1       digest_0.6.18    
[13] viridisLite_0.3.0 tibble_2.0.1      evaluate_0.12    
[16] lattice_0.20-38   pkgconfig_2.0.2   rlang_0.3.1      
[19] Matrix_1.2-15     foreach_1.4.4     rstudioapi_0.9.0 
[22] yaml_2.2.0        parallel_3.5.1    xml2_1.2.0       
[25] httr_1.4.0        stringr_1.3.1     hms_0.4.2        
[28] webshot_0.5.1     rprojroot_1.3-2   grid_3.5.1       
[31] glue_1.3.0        R6_2.3.0          rmarkdown_1.11   
[34] mixsqp_0.1-93     rmeta_3.0         readr_1.3.1      
[37] magrittr_1.5      whisker_0.3-2     scales_1.0.0     
[40] backports_1.1.3   codetools_0.2-16  htmltools_0.3.6  
[43] MASS_7.3-51.1     rvest_0.3.2       abind_1.4-5      
[46] assertthat_0.2.0  colorspace_1.4-0  stringi_1.2.4    
[49] munsell_0.5.0     doParallel_1.0.14 pscl_1.5.2       
[52] truncnorm_1.0-8   SQUAREM_2017.10-1 crayon_1.3.4     
[55] R.oo_1.22.0

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