scripts R des tp1 à 4

src/tp1.R

+options(repos = c(CRAN = "https://cloud.r-project.org"))
+output_dir = "results/tp1"
+dir.create(output_dir, showWarnings = F, recursive = T)
+
+# if (!require("BiocManager", quietly = TRUE))
+#  install.packages("BiocManager")
+
+#if (!require("snpStats", quietly = TRUE))
+#  BiocManager::install("snpStats")
+
+#if (!require("SNPRelate", quietly = TRUE))
+#BiocManager::install("SNPRelate")
+
+# Charger les bibliothèques
+#library(snpStats)
+#library(SNPRelate)
+#library(devtools)
+#library(plyr)
+
+# 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"
+penncath_fam_path = "results/data/penncath.fam"
+
+geno <- snpStats::read.plink(penncath_bed_path, penncath_bim_path, penncath_fam_path, select.snps=sample(1:861473, 25000, replace = FALSE ), na.strings = ("-9"))
+
+plink_base=file.path(output_dir, "plink_base")
+snpStats::write.plink(plink_base, snps=geno$genotypes, pedigree=geno$fam[,1], id=geno$fam[,1], mother=geno$fam[,4], sex=geno$fam[,5], phenotype=geno$fam[,6], chromosome = geno$map[,1], genetic.distance = geno$map[,3], position = geno$map[,4], allele.1 = geno$map[,5], allele.2 = geno$map[,6], na.code = ("-9"))
+
+genoBim<-geno$map
+colnames(genoBim)<-c("chr", "SNP", "gen.dist", "position", "A1", "A2")
+#head(genoBim)
+
+genotype<-geno$genotype
+#print(genotype)
+
+genoFam<-geno$fam
+#head(genoFam)
+
+# On commence par libérer de l'espace
+rm(geno)
+
+rdata_path = file.path(output_dir, "TP1_asbvg.RData")
+save.image(rdata_path)
+

src/tp2.R

-wdir="/amuhome/t20006223/m2bsgreprod/src"
-dir.create(wdir)
-setwd(wdir)
+#load data
+load("results/tp1/TP1_asbvg.RData")
 
-library(devtools)
+#fichier de sortie
+output_dir = "results/tp2"
+dir.create(output_dir, showWarnings = F, recursive = T)
+
+#on installe et ouvre les packages/librairies nécessaires
 
 if (!require("BiocManager", quietly=TRUE))
   install.packages("BiocManager")
 
-if (!require("snpStats", quietly=TRUE))
-  BiocManager::install("snpStats")
-
 if (!require("SNPRelate", quietly=TRUE))
   BiocManager::install("SNPRelate")
 
-library(snpStats)
+#on enregistre le fichier de sortie 
 
-library(SNPRelate)
+rdata_path = file.path(output_dir, "TP2_asbvg.RData")
+save.image(rdata_path)
 
-# Les données analysées nécessitant beaucoup de RAM, nous allons sélectionner aléatoirement 250000 SNPs et réecrire des fichiers bed, bim, fam
-penncath_bed_path = "/amuhome/t20006223/m2bsgreprod/results/data/penncath.bed"
-penncath_bim_path = "/amuhome/t20006223/m2bsgreprod/results/data/penncath.bim"
-penncath_fam_path = "/amuhome/t20006223/m2bsgreprod/results/data/penncath.fam"
-geno <- snpStats::read.plink(penncath_bed_path, penncath_bim_path, penncath_fam_path, select.snps=sample(1:861473, 25000, replace = FALSE ), na.strings = ("-9"))

src/tp3.R

+#load data
+load("results/tp2/TP2_asbvg.RData")
+
+#fichier de sortie
+output_dir = "results/tp3"
+dir.create(output_dir, showWarnings = F, recursive = T)
+
+#library
+if (!require("BiocManager", quietly = TRUE))
+  install.packages("BiocManager")
+
+if (!require("snpStats", quietly = TRUE))
+  BiocManager::install("snpStats")
+
+#if (!require("doParallel", quietly = TRUE))
+ # BiocManager::install("doParallel")
+
+library(snpStats)
+library(plyr)
+library(GenABEL)
+#library(doParallel)
+
+rdata_path = file.path(output_dir,"TP3_asbvg.RData")
+save.image(rdata_path)
+

src/tp4.R

+#load data
+load("results/tp3/TP3_asbvg.RData")
+
+#fichier de sortie
+output_dir = "results/tp4"
+dir.create(output_dir, showWarnings = F, recursive = T)
+
+#Library
+if(!require("dplyr",quietly = T))
+  install.packages("dplyr")
+
+if(!require("plyr",quietly = T))
+  install.packages("plyr")
+
+if(!require("GenABEL",quietly = T))
+  install.packages("GenABEL")
+
+rdata_path = file.path(output_dir,"TP4_asbvg.RData")
+save.image(rdata_path)
+