From 897adf980048bf410983aae402e32a17231e50fb Mon Sep 17 00:00:00 2001
From: SOLER Fiona <s23014817@V-PJ-47-058.salsa.univ-amu.fr>
Date: Wed, 23 Oct 2024 14:15:17 +0200
Subject: [PATCH] suppression
---
sources/.Rhistory | 2 --
sources/download_data.R | 54 -----------------------------------------
sources/tp2.R | 27 ---------------------
3 files changed, 83 deletions(-)
delete mode 100644 sources/.Rhistory
delete mode 100644 sources/download_data.R
delete mode 100644 sources/tp2.R
diff --git a/sources/.Rhistory b/sources/.Rhistory
deleted file mode 100644
index 7de21e4..0000000
--- a/sources/.Rhistory
+++ /dev/null
@@ -1,2 +0,0 @@
-if (!require("SNPRelate", quietly = TRUE))
-BiocManager::install("SNPRelate")
diff --git a/sources/download_data.R b/sources/download_data.R
deleted file mode 100644
index 61e5291..0000000
--- a/sources/download_data.R
+++ /dev/null
@@ -1,54 +0,0 @@
-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!")
-}
-
-
-
diff --git a/sources/tp2.R b/sources/tp2.R
deleted file mode 100644
index edc229b..0000000
--- a/sources/tp2.R
+++ /dev/null
@@ -1,27 +0,0 @@
-
-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"))
-
-
-
-
--
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