From 3b3fa4c2ebdc15411f79c98f2f21292abae2e3ca Mon Sep 17 00:00:00 2001
From: TRON Kelly <t19016063@V-PJ-47-066.salsa.univ-amu.fr>
Date: Wed, 23 Oct 2024 14:07:21 +0200
Subject: [PATCH] tp1
---
doc/{01install.md => install} | 0
src/.Rhistory | 10 ++++++++++
workflows/.Rhistory | 0
workflows/Makefile | 16 ++++++++++++++++
4 files changed, 26 insertions(+)
rename doc/{01install.md => install} (100%)
create mode 100644 src/.Rhistory
create mode 100644 workflows/.Rhistory
create mode 100644 workflows/Makefile
diff --git a/doc/01install.md b/doc/install
similarity index 100%
rename from doc/01install.md
rename to doc/install
diff --git a/src/.Rhistory b/src/.Rhistory
new file mode 100644
index 0000000..53e6de6
--- /dev/null
+++ b/src/.Rhistory
@@ -0,0 +1,10 @@
+# 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"))
+# Les données analysées nécessitant beaucoup de RAM, nous allons sélectionner aléatoirement 250000 SNPs et réecrire des fichiers bed, bim, fam
+penncath_bed_path = "~/Bureau/project_reprod/m2reprod/results/data/penncath.bed"
+penncath_bim_path = "~/Bureau/project_reprod/m2reprod/results/data/penncath.bim"
+penncath_fam_path = "~/Bureau/project_reprod/m2reprod/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"))
diff --git a/workflows/.Rhistory b/workflows/.Rhistory
new file mode 100644
index 0000000..e69de29
diff --git a/workflows/Makefile b/workflows/Makefile
new file mode 100644
index 0000000..0dfdbdd
--- /dev/null
+++ b/workflows/Makefile
@@ -0,0 +1,16 @@
+# Makefile
+all : results/tp3/TP3_asbvg.RData
+
+results/tp3/TP3_asbvg.RData: results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData
+ Rscript src/tp1.R
+
+results/tp1/plink_base.bed results/tp1/plink_base.bim results/tp1/plink_base.fam results/tp1/TP1_asbvg.RData: results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam
+ Rscript src/tp1.R
+
+results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam:
+ Rscript src/download_data.R
+
+clean:
+ rm -rf results/data/penncath.bed results/data/penncath.bim results/data/penncath.fam results/data/penncath.csv results/penncath.tar.gz results/data
+
+
--
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