Set up data

library(lattice)
library(ggplot2)
library(mashr)

Loading required package: ashr

load('../data/processed.RData')
source("../code/multiplot.R")
gene.names.pro = processed.data$ctrl$V4
data = readRDS('../data/ImmuneQTLSummary.4MASH.rds')
data$max$se = data$max$beta/data$max$z
data$null$se = data$null$beta / data$null$z
gene.names.data = substr(row.names(data$max$beta),1,12)

K = 10
P = 5
vhat = 1
thre = 0.01

MASH results

# EZ
resEZ = readRDS('../output/ImmuneEZ.V1.center.mash_model.K10.P5.rds')
resEZ$result = readRDS('../output/ImmuneEZ.V1.center.mash_posterior.K10.P5.rds')

eQTL index in each group

eQTL.index.mash = list(base=get_significant_results(resEZ, conditions=1),
                       lps6h=get_significant_results(resEZ, conditions=2),
                       lps90=get_significant_results(resEZ, conditions=3),
                       mdp6h=get_significant_results(resEZ, conditions=4),
                       mdp90=get_significant_results(resEZ, conditions=5),
                       rna6h=get_significant_results(resEZ, conditions=6),
                       rna90=get_significant_results(resEZ, conditions=7))

Session information

sessionInfo()

R version 3.4.2 (2017-09-28)
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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] mashr_0.2-4     ashr_2.1-27     ggplot2_2.2.1   lattice_0.20-35

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14      compiler_3.4.2    git2r_0.19.0     
 [4] plyr_1.8.4        iterators_1.0.8   tools_3.4.2      
 [7] digest_0.6.12     evaluate_0.10.1   tibble_1.3.4     
[10] gtable_0.2.0      rlang_0.1.2       Matrix_1.2-11    
[13] foreach_1.4.3     yaml_2.1.14       parallel_3.4.2   
[16] mvtnorm_1.0-6     stringr_1.2.0     knitr_1.17       
[19] rprojroot_1.2     rmarkdown_1.7     rmeta_2.16       
[22] magrittr_1.5      backports_1.1.1   scales_0.5.0     
[25] codetools_0.2-15  htmltools_0.3.6   MASS_7.3-47      
[28] assertthat_0.2.0  colorspace_1.3-2  labeling_0.3     
[31] stringi_1.1.5     lazyeval_0.2.1    munsell_0.4.3    
[34] doParallel_1.0.11 pscl_1.5.2        truncnorm_1.0-7  
[37] SQUAREM_2017.10-1