diff --git a/src/tp1.R b/src/tp1.R new file mode 100644 index 0000000000000000000000000000000000000000..44b14f311b1cadf89e0651bbdabe4c9b3cef90dc --- /dev/null +++ b/src/tp1.R @@ -0,0 +1,45 @@ +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) +