R/setup_sims.R

In jean997/causeSims: Generate Summary Statistic Data and Analyze with a Variety of MR Methods

#'@title Set up simulation directory
#'@description A helper function that prepares a working directory for running simulations.
#'@details This function prepares a working directory to replicate the simulations presented in Morrison et al 2019
#'(https://www.biorxiv.org/content/10.1101/682237v3). After running this function you will be able to execute simulation
#'experiments using DSC using the commands
#'
#'  nohup dsc --replicate 100 --host config.yml -c 4 [dscfile] > [outputfile] &
#'
#'
#'  You will need to modify the config.yml file to work with your compute cluster.
#'@export
setup_sims <- function(){
  #Download DSC files
  cat("Downloading DSC files\n")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/dsc_files/power.dsc" , destfile="power.dsc")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/dsc_files/false_positives.dsc" , destfile="false_positives.dsc")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/dsc_files/reverse.dsc" , destfile="reverse.dsc")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/dsc_files/mixture1.dsc" , destfile="mixture1.dsc")
  #Download data
  if(!dir.exists("data/")) system("mkdir data")
  cat("Downloading LD Data\n")
  download.file(url="https://zenodo.org/record/3235780/files/chr19_snpdata_hm3only.RDS?download=1", destfile = "data/chr19_snpdata_hm3only.RDS")
  download.file(url="https://zenodo.org/record/3235780/files/evd_list_chr19_hm3.RDS?download=1", destfile="data/evd_list_chr19_hm3.RDS")

  cat("Downloading config file. You will need to modify this for your setup\n")
  download.file(url="https://raw.githubusercontent.com/jean997/causeSims/master/dsc_files/config.yml", destfile="config.yml")

  #Download Results
  cat("Downloading Results\n")
  if(!dir.exists("sim_results/")) system("mkdir sim_results")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/results/res_pwr.RDS" , destfile="sim_results/res_pwr.RDS")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/results/res_fp.RDS" , destfile="sim_results/res_fp.RDS")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/results/res_rev.RDS" , destfile="sim_results/res_rev.RDS")
  download.file(url = "https://raw.githubusercontent.com/jean997/causeSims/master/results/res_mix1.RDS" , destfile="sim_results/res_mix1.RDS")

  #cat("Results are not available now but will be soon.\n")
  #download.file(url = "https://zenodo.org/record/3350911/files/main_causedf.RDS?download=1", destfile="sim_results/main_causedf.RDS")
  #download.file(url = "https://zenodo.org/record/3350911/files/main_lcvdf.RDS?download=1", destfile="sim_results/main_lcvdf.RDS")
  #download.file(url = "https://zenodo.org/record/3350911/files/main_mrdf.RDS?download=1", destfile="sim_results/main_mrdf.RDS")
  #download.file(url = "https://zenodo.org/record/3350911/files/sg_causedf.RDS?download=1", destfile="sim_results/sg_causedf.RDS")

}