Last updated: 2019-10-09

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Knit directory: MMVBVS/

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Load Package


Create Data

beta = c(seq(0.1, 0.5, length=5), rep(0,5))
n = 500; T = length(beta); nu = T+5
Sigma = matrix(0.8, T, T); diag(Sigma) = 1
X = as.numeric(scale(rnorm(n)))
error = MASS::mvrnorm(n, rep(0,T), Sigma)
gamma = c(rep(1,5), rep(0,5))
Y = X %*% t(beta) + error; Y = scale(Y)
for (i in 1:10){
  Y[sample(1:400, 200), i] = NA

Run Algorithm

Phi = matrix(0.5, T, T); diag(Phi) = 1
initial_chain = list(beta = rep(0,T), 
                      gamma = rep(0,T), 
                      Sigma = Phi, 
                      sigmabeta = 1)
result = mmvbvs(X = X,
                Y = Y,
                initial_chain = initial_chain,
                Phi = Phi,
                marcor = colMeans(X*Y, na.rm=TRUE),
                sigmabeta = 1,
                verbose = FALSE)

Analyze Result

Inclusion of each tissue by iterations

plot_gamma(result, title = "")

Version Author Date
4f4fc15 tk382 2019-10-08

Trajectory of \(\beta\) by iterations

plot_beta(result, title="")

Version Author Date
4f4fc15 tk382 2019-10-08

Posterior Distribution of the coefficients \(\beta\)

beta_dist(result, title="")

Version Author Date
4f4fc15 tk382 2019-10-08

Heatmap of Posterior Mean of \(\Sigma\)

plot_sigma(result, title="")

R version 3.5.3 (2019-03-11)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

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

[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] ggplot2_3.1.0 MMVBVS_0.1.0 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1       compiler_3.5.3   pillar_1.3.1     git2r_0.25.2    
 [5] plyr_1.8.4       workflowr_1.2.0  tools_3.5.3      digest_0.6.18   
 [9] evaluate_0.13    tibble_2.1.1     gtable_0.3.0     pkgconfig_2.0.2 
[13] rlang_0.3.3      yaml_2.2.0       xfun_0.5         withr_2.1.2     
[17] stringr_1.4.0    dplyr_0.8.0.1    knitr_1.22       fs_1.2.7        
[21] rprojroot_1.3-2  grid_3.5.3       tidyselect_0.2.5 reshape_0.8.8   
[25] glue_1.3.1       R6_2.4.0         rmarkdown_1.12   purrr_0.3.2     
[29] reshape2_1.4.3   magrittr_1.5     whisker_0.3-2    backports_1.1.3 
[33] scales_1.0.0     htmltools_0.3.6  MASS_7.3-51.3    assertthat_0.2.1
[37] colorspace_1.4-1 labeling_0.3     stringi_1.4.3    lazyeval_0.2.2  
[41] munsell_0.5.0    crayon_1.3.4