From 1246ab66589135d4511fc892f63e5dab69d0a54f Mon Sep 17 00:00:00 2001
From: Natan Yusupov <natan_yusupov@psych.mpg.de>
Date: Thu, 14 Mar 2024 14:53:33 +0100
Subject: [PATCH] small bug fix script 2

---
 scripts/2_import_raw_DNAm_data.Rmd | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scripts/2_import_raw_DNAm_data.Rmd b/scripts/2_import_raw_DNAm_data.Rmd
index 8da92d3..7569720 100644
--- a/scripts/2_import_raw_DNAm_data.Rmd
+++ b/scripts/2_import_raw_DNAm_data.Rmd
@@ -24,6 +24,8 @@ if (any(installed_biocmanager_packages == FALSE)) {
 }
 lapply(needed_biocmanager_packages, library, character.only = TRUE)
 
+user_choices <- readRDS("../data/user_choices.rds")
+
 if (user_choices$array_type == "v2") {
   if (!("jokergoo/IlluminaHumanMethylationEPICv2manifest" %in% rownames(installed.packages()))) {
     BiocManager::install("jokergoo/IlluminaHumanMethylationEPICv2manifest")
@@ -35,7 +37,6 @@ if (user_choices$array_type == "v2") {
   library(IlluminaHumanMethylationEPICv2anno.20a1.hg38)
 }
 
-user_choices <- readRDS("../data/user_choices.rds")
 knitr::opts_knit$set(root.dir = paste0(user_choices$personal_path, "/"))
 knitr::opts_chunk$set(echo = FALSE)
 ```