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    tp2.R 910 B 
    wdir="/amuhome/t20006223/m2bsgreprod/src"
dir.create(wdir)
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")

library(snpStats)

library(SNPRelate)

# 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"))