From 44f21ac6a9e8a6757c5a9a4b627717bc3f88a91d Mon Sep 17 00:00:00 2001
From: KHAM Chaimae <k24022051@V-PP-47-L-003.salsa.univ-amu.fr>
Date: Mon, 28 Oct 2024 14:38:23 +0100
Subject: [PATCH] modification de fichiers
---
src/tp1.R | 10 ++++------
src/tp3.R | 6 +++---
src/tp4.R | 12 ++++++------
workflow/makefile | 23 +++++++++--------------
4 files changed, 22 insertions(+), 29 deletions(-)
diff --git a/src/tp1.R b/src/tp1.R
index 0b81760..0f3e01b 100644
--- a/src/tp1.R
+++ b/src/tp1.R
@@ -2,7 +2,7 @@ options(repos = c(CRAN = "https://cloud.r-project.org"))
output_dir = "results/tp1"
dir.create(output_dir, showWarnings = F, recursive = T)
-<<<<<<< HEAD
+
# if (!require("BiocManager", quietly = TRUE))
# install.packages("BiocManager")
@@ -18,8 +18,6 @@ dir.create(output_dir, showWarnings = F, recursive = T)
#library(devtools)
#library(plyr)
-=======
->>>>>>> main
# Les données analysées nécessitant beaucoup de RAM, nous allons sélectionner aléatoirement 250000 SNPs et réecrire des fichiers bed, bim, fam
penncath_bed_path = "results/data/penncath.bed"
penncath_bim_path = "results/data/penncath.bim"
@@ -46,8 +44,8 @@ rm(geno)
rdata_path = file.path(output_dir, "TP1_asbvg.RData")
save.image(rdata_path)
-<<<<<<< HEAD
-=======
->>>>>>> main
+
+
+
diff --git a/src/tp3.R b/src/tp3.R
index d7c176f..94f2f04 100644
--- a/src/tp3.R
+++ b/src/tp3.R
@@ -12,13 +12,13 @@ if (!require("BiocManager", quietly = TRUE))
if (!require("snpStats", quietly = TRUE))
BiocManager::install("snpStats")
-if (!require("doParallel", quietly = TRUE))
- BiocManager::install("doParallel")
+#if (!require("doParallel", quietly = TRUE))
+ # BiocManager::install("doParallel")
library(snpStats)
library(plyr)
library(GenABEL)
-library(doParallel)
+#library(doParallel)
rdata_path = file.path(output_dir,"TP3_asbvg.RData")
save.image(rdata_path)
diff --git a/src/tp4.R b/src/tp4.R
index 8934080..7b6d3be 100644
--- a/src/tp4.R
+++ b/src/tp4.R
@@ -6,14 +6,14 @@ output_dir = "results/tp4"
dir.create(output_dir, showWarnings = F, recursive = T)
#Library
-if(!require("dplyr",quietly = T))
- install.packages("dplyr")
+#if(!require("dplyr",quietly = T))
+ # install.packages("dplyr")
-if(!require("plyr",quietly = T))
- install.packages("plyr")
+#if(!require("plyr",quietly = T))
+ #install.packages("plyr")
-if(!require("GenABEL",quietly = T))
- install.packages("GenABEL")
+#if(!require("GenABEL",quietly = T))
+ #install.packages("GenABEL")
rdata_path = file.path(output_dir,"TP4_asbvg.RData")
save.image(rdata_path)
diff --git a/workflow/makefile b/workflow/makefile
index c863e10..32f14a6 100644
--- a/workflow/makefile
+++ b/workflow/makefile
@@ -1,20 +1,15 @@
-all: results/tp4/TP4_asbvg.RData
-
-results/tp4/TP4_asbvg.RData: results/tp3/TP3_asbvg.RData
+all:results/tp4/TP4_asbvg.RData
Rscript src/tp4.R
-
-results/tp3/TP3_asbvg.RData: results/tp2/TP2_asbvg.RData
+
+results/tp4/TP4_asbvg.RData:results/tp3/TP3_asbvg.RData
Rscript src/tp3.R
-
-results/tp2/TP2_asbvg.RData: results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData
+
+results/tp3/TP3_asbvg.RData:results/tp2/TP2_asbvg.RData
Rscript src/tp2.R
-
-results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData: results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam
+
+results/tp2/TP2_asbvg.RData:results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData
Rscript src/tp1.R
-
-results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam:
- Rscript src/download_data.R
-clean:
- rm -rf results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam results/data/penncath.csv results/penncath.tar.gz results/data
+results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData:results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam
+ Rscript src/download_data.R
--
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