suppression

sources/.Rhistory

-if (!require("SNPRelate", quietly = TRUE))
-BiocManager::install("SNPRelate")

sources/download_data.R

-options(repos = c(CRAN = "https://cloud.r-project.org"))
-
-# Install 'remotes' if it's not already installed
-if (!require("remotes")) {
-  install.packages("remotes", dependencies = TRUE)
-  library(remotes)
-}
-
-# Load necessary library and install a specific version if not present
-if (!requireNamespace("digest", quietly = TRUE)) {
-  remotes::install_version("digest", version = "0.6.25", repos = "https://cloud.r-project.org")
-}
-# Load necessary library
-if (!require("digest")) install.packages("digest", dependencies = TRUE)
-library(digest)
-
-# Define variables
-# wdir="/shared/projects/2427_data_master/user/agonzalez/m2bsgreprod/src"
-wdir="."
-results_dir <- file.path(wdir, "results")
-url <- "https://d1ypx1ckp5bo16.cloudfront.net/penncath/penncath.tar.gz"
-dest_file <- file.path(results_dir, "penncath.tar.gz")
-expected_md5 <- "5d5f422aeafdd2d725ad93f447d9af4b"
-
-# Create results directory if it doesn't exist
-if (!dir.exists(results_dir)) {
-  dir.create(results_dir, recursive = TRUE)
-}
-
-# Check if the file exists
-if (!file.exists(dest_file)) {
-  message("File does not exist. Downloading...")
-  # Download the file
-  download.file(url, dest_file, method = "auto")
-} else {
-  message("File already exists.")
-}
-
-# Verify the MD5 checksum
-actual_md5 <- digest(dest_file, algo = "md5", file = TRUE)
-
-if (actual_md5 == expected_md5) {
-  message("MD5 checksum matches! Proceeding to extract the file...")
-  
-  # Uncompress the file
-  untar(dest_file, exdir = results_dir)
-  message("File uncompressed successfully!")
-  
-} else {
-  stop("MD5 checksum does not match!")
-}
-
-
-

sources/tp2.R

-
-wdir ="/amuhome/s23014817/m2bsgreprod/sources"
-dir.create(wdir, showWarnings = F, recursive = T)
-setwd(wdir)
-
-library(devtools)
-
-if (!require("BiocManager", quietly = TRUE)) #boucle qui permet de dire que s'il n'est pas installé il faut l'installer mais s'il est déjà installé pas besoin 
-  install.packages("BiocManager")
-
-if (!require("snpStats", quietly = TRUE))
-  BiocManager::install("snpStats")
-
-if (!require("SNPRelate", quietly = TRUE))
-  BiocManager::install("SNPRelate")
-
-
-
-# Les données analysées nécessitant beaucoup de RAM, nous allons sélectionner aléatoirement 250000 SNPs et réecrire des fichiers bed, bim, penncath
-penncath_bed_path = "/amuhome/s23014817/m2bsgreprod/results/data/penncath.bed"
-penncath_bim_path = "/amuhome/s23014817/m2bsgreprod/results/data/penncath.bim"
-penncath_fam_path = "/amuhome/s23014817/m2bsgreprod/results/data/penncath.fam"
-geno <- read.plink(penncath_bed_path, penncath_bim_path, penncath_fam_path, select.snps=sample(1:861473, 25000, replace = FALSE ), na.strings = ("-9"))
-
-
-
-