script

src/tp1.R

+wdir="."
+dir.create(wdir, showWarnings = F, recursive = T)
+setwd(wdir)
+
+#library(devtools)
+
+if (!require("BiocManager", quietly = TRUE))
+  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, 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"))
+
+