R/init.R

In Chris1221/coRge: An R package for the Examination of Multiple Correction Methodologies in Accurate Genomic Environments.

#' Initialize a testing environment
#'
#' This is definitely not working yet
#'
#' @export

init <- function(){
	library(dplyr)
	library(data.table)
	library(magrittr)
	library(foreach)
	library(devtools)

	setwd("/scratch/hpc2862/CAMH/perm_container")

	i <-  double()
	j <- double()
	#mode <<- "default"
	path.base <- "/scratch/hpc2862/CAMH/perm_container/container_"
	summary.file <- "/scratch/hpc2862/CAMH/perm_container/snp_summary2.out"
	output <- "~/repos/coR-ge/data/test_run2.txt"
	test <- TRUE
	safe <- TRUE

	vold <- packageVersion("coRge")

	if(!require(devtools)) install.packages("devtools")
	devtools::install_github("Chris1221/coR-ge", ref = "devel")

	vnew <- packageVersion("coRge")

	if(vold != vnew) message("coRge has been updated!")

	return(list(i,j, path.base, summary.file, output, test, safe))
}