From 1246ab66589135d4511fc892f63e5dab69d0a54f Mon Sep 17 00:00:00 2001 From: Natan Yusupov 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) ```