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tp1.R

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    tp1.R 790 B 
    wdir="."
dir.create(<dir, 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"))