Last updated: 2017-03-03

Code version: 11b31d3

The following code reads in Vhat from the “nullish” z scores, and checks they exceed the lower bound from here. If not it replaces them with the lower bound.

source("../code/SumstatQuery.R")
  ##
  # Load data for a random subset of eqtls
  dat <- GetSS("null", "../data/MatrixEQTLSumStats.Portable.h5")
  vhat = readRDS("../data/vhat.RDS")
  vhat = ifelse(vhat<0, 0,vhat)
  for(i in 1:(nrow(vhat)-1)){
    for(j in (i+1):ncol(vhat)){
      lb = 1-0.5*mean((dat$z[,i]-dat$z[,j])^2)
      if(vhat[i,j]<lb){vhat[i,j]=lb} #set to lower bound if lower than lower bound
      vhat[j,i] = vhat[i,j]
    }
  }
  
  saveRDS(vhat,"../data/vhat.lb.RDS")
  dimnames(vhat)=NULL #had to do this to make the figure nice
  corrplot::corrplot(as.matrix(vhat),xlab="")

Session Information

sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.6

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] RSQLite_1.1-2 rhdf5_2.18.0 

loaded via a namespace (and not attached):
 [1] workflowr_0.3.0 Rcpp_0.12.9     digest_0.6.12   rprojroot_1.2   DBI_0.5-1       backports_1.0.5 git2r_0.18.0   
 [8] magrittr_1.5    evaluate_0.10   stringi_1.1.2   zlibbioc_1.20.0 rstudioapi_0.6  rmarkdown_1.3   tools_3.3.2    
[15] stringr_1.2.0   yaml_2.1.14     corrplot_0.77   memoise_1.0.0   htmltools_0.3.5 knitr_1.15.1

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