Skip to content
Snippets Groups Projects
Commit 897adf98 authored by SOLER Fiona's avatar SOLER Fiona
Browse files

suppression

parent dbba0f75
No related branches found
No related tags found
No related merge requests found
if (!require("SNPRelate", quietly = TRUE))
BiocManager::install("SNPRelate")
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!")
}
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"))
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment