Starter.R

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#Title:    G-WASPiper-Starter.R
#Function: Install packages and create folders
#Author:   Murat Guler (murat.guler@dkfz.de, muratgmbg@gmail.com)
#Date:     Dec 29th 2023
#Note:     Please let me know if you have any trouble
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# Optinal to clean your memory/workspace
rm(list = ls())
gc()
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# Install and check necessary package(s)
# Vector of package names
packages <- c("tidyverse", "data.table", "dplyr", "ggplot2")

# Install and load packages
for (pkg in packages) {
  if (!requireNamespace(pkg, quietly = TRUE)) {
    install.packages(pkg)
  }
  library(pkg, character.only = TRUE)
}
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# Download scripts that needed, please update file names or URL in the scripts
system("git clone https://github.com/biomguler/G-WASPiper.git")
#update if needed
system("unzip G-WASPiper.zip")

# Create folders for outputs
system("mkdir final2plink")
system("mkdir raw_plink")
system("mkdir QCsteps")
system("mkdir 1000G")
system("mkdir results")
system("mkdir final")
system("mkdir topmed")
system("mkdir PGS")
# Optinal to clean your memory/workspace
rm(list = ls())
gc()
#End