From 33d5fa001e4625c808518b48f8dbf23b6659b1f0 Mon Sep 17 00:00:00 2001
From: TRON Kelly <t19016063@V-PJ-47-066.salsa.univ-amu.fr>
Date: Wed, 23 Oct 2024 16:23:10 +0200
Subject: [PATCH] tp1
---
src/tp1.R | 12 +++++++-----
1 file changed, 7 insertions(+), 5 deletions(-)
diff --git a/src/tp1.R b/src/tp1.R
index 904a363..44b14f3 100644
--- a/src/tp1.R
+++ b/src/tp1.R
@@ -1,16 +1,17 @@
+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("BiocManager", quietly = TRUE))
+# install.packages("BiocManager")
#if (!require("snpStats", quietly = TRUE))
- # BiocManager::install("snpStats")
+# BiocManager::install("snpStats")
#if (!require("SNPRelate", quietly = TRUE))
#BiocManager::install("SNPRelate")
-#Charger les bibliothèques
+# Charger les bibliothèques
#library(snpStats)
#library(SNPRelate)
#library(devtools)
@@ -24,7 +25,7 @@ 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")
-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$map[,6], na.code = ("-9"))
+snpStats::write.plink(plink_base, snps=geno$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")
@@ -41,3 +42,4 @@ rm(geno)
rdata_path = file.path(output_dir, "TP1_asbvg.RData")
save.image(rdata_path)
+
--
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